Pierre GrenonBjoern PetersMatthew PocockLiju FanChristian BollingChris TaylorChris StoeckertPlease cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.2017-11-07Tina Hernandez-BoussardJessica TurnerAllyson ListerYongqun HeJie ZhengTanya Gray2009-07-31Bill BugAdvisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in ManchesterLawrence HunterThe Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.Chris MungallDaniel SchoberHelen C. CaustonJames MaloneKevin ClancySusanna-Assunta SansoneNorman MorrisonDaniel RubinCristian CocosStefan WiemannAn ontology for the annotation of biomedical and functional genomics experiments.Melanie CourtotHelen ParkinsonJeffrey GretheJennifer FostelLuisa MontecchiEric DeutschOntology for Biomedical InvestigationPhilip LordGilberto FragosoPhilippe Rocca-SerraElisabetta ManduchiOWL-DLMervi HeiskanenRichard BruskiewichRobert StevensDirk DeromLarisa SoldatovaJames A. OvertonDawn FieldTrish WhetzelAlan RuttenbergFrank GibsonMatthew BrushRichard ScheuermannJohn WestbrookBarry SmithCarlo TorniaienJay GreenbaumRyan R. BrinkmanMonnie McGeeHolger StenzhornMelissa HaendelJoe WhiteRelates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.Really of interest to developers onlyBFO OWL specification labelRelates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2Person:Alan RuttenbergReally of interest to developers onlyBFO CLIF specification labeleditor preferred labeleditor preferred labeleditor preferred termeditor preferred termeditor preferred term~editor preferred labelThe concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)PERSON:Daniel SchoberGROUP:OBI:<http://purl.obolibrary.org/obo/obi>editor preferred labeleditor preferred labeleditor preferred termeditor preferred termeditor preferred term~editor preferred labelexampleA phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.PERSON:Daniel SchoberGROUP:OBI:<http://purl.obolibrary.org/obo/obi>example of usagein branchAn annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.GROUP:OBIOBI_0000277in branchhas curation statusPERSON:Alan RuttenbergPERSON:Bill BugPERSON:Melanie CourtotOBI_0000281has curation statusdefinitiondefinitiondefinitiontextual definitiontextual definitionThe official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel SchoberGROUP:OBI:<http://purl.obolibrary.org/obo/obi>definitiondefinitiondefinitiontextual definitiontextual definitioneditor noteAn administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.PERSON:Daniel SchoberGROUP:OBI:<http://purl.obfoundry.org/obo/obi>editor noteterm editorName of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.PERSON:Daniel SchoberGROUP:OBI:<http://purl.obolibrary.org/obo/obi>term editoralternative termAn alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)PERSON:Daniel SchoberGROUP:OBI:<http://purl.obolibrary.org/obo/obi>alternative termdefinition sourceformal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007PERSON:Daniel SchoberDiscussion on obo-discuss mailing-list, see http://bit.ly/hgm99wGROUP:OBI:<http://purl.obolibrary.org/obo/obi>definition sourcehas obsolescence reasonRelates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.PERSON:Alan RuttenbergPERSON:Melanie Courtothas obsolescence reasoncurator noteAn administrative note of use for a curator but of no use for a userPERSON:Alan Ruttenbergcurator noteterm tracker itemthe URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/An IRI or similar locator for a request or discussion of an ontology term.Person: Jie Zheng, Chris Stoeckert, Alan RuttenbergPerson: Jie Zheng, Chris Stoeckert, Alan RuttenbergThe 'tracker item' can associate a tracker with a specific ontology term.term tracker itemThe name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.Person: Jie Zheng, Chris Stoeckert, Alan RuttenbergPerson: Jie Zheng, Chris Stoeckert, Alan RuttenbergThe 'term requester' can credit the person, organization or project who request the ontology term.ontology term requesteris denotator typerelates an class defined in an ontology, to the type of it's denotatorIn OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')Alan Ruttenbergis denotator typeimported fromFor external terms/classes, the ontology from which the term was importedPERSON:Alan RuttenbergPERSON:Melanie CourtotGROUP:OBI:<http://purl.obolibrary.org/obo/obi>imported fromexpand expression toObjectProperty: RO_0002104
Label: has plasma membrane part
Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler onesChris Mungallexpand expression toexpand assertion toObjectProperty: RO???
Label: spatially disjoint from
Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.Chris Mungallexpand assertion tofirst order logic expressionPERSON:Alan Ruttenbergfirst order logic expressionantisymmetric propertypart_of antisymmetric property xsd:trueuse boolean value xsd:true to indicate that the property is an antisymmetric propertyAlan Ruttenbergantisymmetric propertyOBO foundry unique labelAn alternative name for a class or property which is unique across the OBO Foundry.The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .PERSON:Alan RuttenbergPERSON:Bjoern PetersPERSON:Chris MungallPERSON:Melanie CourtotGROUP:OBO Foundry <http://obofoundry.org/>OBO foundry unique labelOntology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)Person:Alan Ruttenberghas ID digit countDatatype: idrange:1
Annotations: 'has ID range allocated to': "Chris Mungall"
EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new termsPerson:Alan Ruttenberghas ID range allocated toOntology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"Relating an ontology used to record id policy to the ontology namespace whose policy it managesPerson:Alan Ruttenberghas ID policy forOntology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.Person:Alan Ruttenberghas ID prefixelucidationperson:Alan RuttenbergPerson:Barry SmithPrimitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axiomselucidationhas associated axiom(nl)Person:Alan RuttenbergPerson:Alan RuttenbergAn axiom associated with a term expressed using natural languagehas associated axiom(nl)has associated axiom(fol)Person:Alan RuttenbergPerson:Alan RuttenbergAn axiom expressed in first order logic using CLIF syntaxhas associated axiom(fol)is allocated id rangeAdd as annotation triples in the granting ontologyRelates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"PERSON:Alan Ruttenbergis allocated id rangeretired from use as ofrelates a class of CRID to the date after which further instances should not be made, according to the central authorityIn OWL 2 add AnnotationPropertyRange xsd:dateTimeStampAlan Ruttenbergretired from use as ofhas axiom idPerson:Alan RuttenbergPerson:Alan RuttenbergA URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URIhas axiom labelterm replaced byAdd as annotation triples in the granting ontologyUse on obsolete terms, relating the term to another term that can be used as a substitutePerson:Alan RuttenbergPerson:Alan Ruttenbergterm replaced byISA alternative termAn alternative term used by the ISA tools project (http://isa-tools.org).Requested by Alejandra Gonzalez-Beltran
https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178Person: Alejandra Gonzalez-BeltranPerson: Philippe Rocca-SerraISA tools project (http://isa-tools.org)ISA alternative termNIAID GSCID-BRC alternative termAn alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).PERSON: Chris Stoeckert, Jie ZhengNIAID GSCID-BRC metadata working groupNIAID GSCID-BRC alternative termIEDB alternative termAn alternative term used by the IEDB.PERSON:Randi Vita, Jason Greenbaum, Bjoern PetersIEDBIEDB alternative termFGED alternative termAn alternative term used by the Functional Genomics Data (FGED) Society.PERSON: Chris Stoeckert, Jie ZhengPenn GroupFGED alternative termtemporal interpretationhttps://github.com/oborel/obo-relations/wiki/ROAndTimeExamples of a Contributor include a person, an
organisation, or a service. Typically, the name of a
Contributor should be used to indicate the entity.An entity responsible for making contributions to the
content of the resource.ContributorContributorCoverage will typically include spatial location (a place name
or geographic coordinates), temporal period (a period label,
date, or date range) or jurisdiction (such as a named
administrative entity).
Recommended best practice is to select a value from a
controlled vocabulary (for example, the Thesaurus of Geographic
Names [TGN]) and that, where appropriate, named places or time
periods be used in preference to numeric identifiers such as
sets of coordinates or date ranges.The extent or scope of the content of the resource.CoverageCoverageExamples of a Creator include a person, an organisation,
or a service. Typically, the name of a Creator should
be used to indicate the entity.An entity primarily responsible for making the content
of the resource.CreatorCreatorTypically, Date will be associated with the creation or
availability of the resource. Recommended best practice
for encoding the date value is defined in a profile of
ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.A date associated with an event in the life cycle of the
resource.DateDateDescription may include but is not limited to: an abstract,
table of contents, reference to a graphical representation
of content or a free-text account of the content.An account of the content of the resource.DescriptionDescriptionTypically, Format may include the media-type or dimensions of
the resource. Format may be used to determine the software,
hardware or other equipment needed to display or operate the
resource. Examples of dimensions include size and duration.
Recommended best practice is to select a value from a
controlled vocabulary (for example, the list of Internet Media
Types [MIME] defining computer media formats).The physical or digital manifestation of the resource.FormatFormatRecommended best practice is to identify the resource by means
of a string or number conforming to a formal identification
system.
Example formal identification systems include the Uniform
Resource Identifier (URI) (including the Uniform Resource
Locator (URL)), the Digital Object Identifier (DOI) and the
International Standard Book Number (ISBN).An unambiguous reference to the resource within a given context.Resource IdentifierResource IdentifierRecommended best practice is to use RFC 3066 [RFC3066],
which, in conjunction with ISO 639 [ISO639], defines two-
and three-letter primary language tags with optional
subtags. Examples include "en" or "eng" for English,
"akk" for Akkadian, and "en-GB" for English used in the
United Kingdom.A language of the intellectual content of the resource.LanguageLanguageExamples of a Publisher include a person, an organisation,
or a service.
Typically, the name of a Publisher should be used to
indicate the entity.An entity responsible for making the resource availablePublisherPublisher
Recommended best practice is to reference the resource by means
of a string or number conforming to a formal identification
system.
A reference to a related resource.RelationRelation
Typically, a Rights element will contain a rights
management statement for the resource, or reference
a service providing such information. Rights information
often encompasses Intellectual Property Rights (IPR),
Copyright, and various Property Rights.
If the Rights element is absent, no assumptions can be made
about the status of these and other rights with respect to
the resource.
Information about rights held in and over the resource.Rights ManagementRights ManagementThe present resource may be derived from the Source resource
in whole or in part. Recommended best practice is to reference
the resource by means of a string or number conforming to a
formal identification system.A reference to a resource from which the present resource
is derived.SourceSourceTypically, a Subject will be expressed as keywords,
key phrases or classification codes that describe a topic
of the resource. Recommended best practice is to select
a value from a controlled vocabulary or formal
classification scheme.The topic of the content of the resource.Subject and KeywordsSubject and Keywords
Typically, a Title will be a name by which the resource is
formally known.
A name given to the resource.TitleTitleType includes terms describing general categories, functions,
genres, or aggregation levels for content. Recommended best
practice is to select a value from a controlled vocabulary
(for example, the DCMI Type Vocabulary [DCMITYPE]). To
describe the physical or digital manifestation of the
resource, use the Format element.The nature or genre of the content of the resource.Resource TypeResource Typeshorthandlabellabelis part ofmy brain is part of my body (continuant parthood, two material entities)my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)this day is part of this year (occurrent parthood)a core relation that holds between a part and its wholeEverything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTimeParthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.part_ofpart ofhttp://www.obofoundry.org/ro/#OBO_REL:part_ofhas partmy body has part my brain (continuant parthood, two material entities)my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)this year has part this day (occurrent parthood)a core relation that holds between a whole and its partEverything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTimeParthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.has_parthas partrealized inthis disease is realized in this disease coursethis fragility is realized in this shatteringthis investigator role is realized in this investigationis realized byrealized_in[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the processrealized inrealizesthis disease course realizes this diseasethis investigation realizes this investigator rolethis shattering realizes this fragilityto say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the processrealizespreceded byAn example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.is preceded bypreceded_byhttp://www.obofoundry.org/ro/#OBO_REL:preceded_bypreceded byprecedesprecedesoccurs inb occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at toccurs_inunfolds inunfolds_inParaphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuantoccurs insite of[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at tParaphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuantcontains processhas measurement unit labelThe process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink.
Here the ink + paper is the independent continuant and the carrier is the pattern in the ink.
c = pattern in the ink
b = paper + ink
r = friendc specifically denotes r =def
r is a portion of reality
& c is a particular quality
& c depends specifically on some independent continuant b
& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly.
Marked means there is a changed or additional quality of the bearer - the quality is the information carrier.
Case 1
Memory trace as mark created when reading some description of some friend. The trace can denote.
Case 2
Pattern of ink arrayed on paper as mark when writing down a friend's name
Case 3
Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sensesee https://github.com/information-artifact-ontology/IAO/issues/25&q=denoteAlan RuttenbergSmith, Ceusters, Ruttenberg, 2000 years of philosophyobsolete_specifically denotestrueThis document is about information artifacts and their representationsis_about is a (currently) primitive relation that relates an information artifact to an entity.7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.person:Alan RuttenbergSmith, Ceusters, Ruttenberg, 2000 years of philosophyis aboutAn information artifact IA mentions an entity E exactly when it has a component/part that denotes E7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definitionPERSON: Jonathan ReesPerson: Alan RuttenbergmentionsA person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.
g denotes r =def
r is a portion of reality
there is some c that is a concretization of g
every c that is a concretization of g specifically denotes rperson:Alan RuttenbergConversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogandenotessee https://github.com/information-artifact-ontology/IAO/issues/25&q=denoteobsolete_materially denotestruem is a quality measurement of q at t when
q is a quality
there is a measurement process p that has specified output m, a measurement datum, that is about q8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing laterFrom the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
--
From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]
unit of measure is a quality, e.g. the length of a ruler.
[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]
[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]
a represents b means either a denotes b or a describes
describe:
a describes b means a is about b and a allows an inference of at least one quality of b
We have had a long discussion about denotes versus describes.From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.
a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.From the second meeting on IAO:
An attempt at defining assay using Barry's "reliability" wording
assay:
process and has_input some material entity
and has_output some information content entity
and which is such that instances of this process type reliably generate
outputs that describes the input.This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.Alan Ruttenbergis quality measurement ofobsolete_describestrueobsolete_representstruerelating a cartesian spatial coordinate datum to a unit label that together with the values represent a pointhas coordinate unit labelrelates a process to a time-measurement-datum that represents the duration of the processPerson:Alan Ruttenbergis duration ofinverse of the relation of is quality measurement of2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationshipPerson:Alan Ruttenbergis quality measured asa relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.Person:Alan RuttenbergPerson:Bjoern Petersis quality specification ofinverse of the relation of is quality specification of2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationshipPerson:Alan RuttenbergPerson:Bjoern Petersquality is specified asrelates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was takenAlan Ruttenberghas time stamprelates a time stamped measurement datum to the measurement datum that was measuredAlan Ruttenberghas measurement datumprovides_service_consumer_withThe provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client.A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.provides_service_consumer_withis_supported_by_dataThe relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that processOBIOBIPhilly 2011 workshopis_supported_by_datahas_specified_inputhas_specified_inputsee is_input_of example_of_usageA relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.PERSON: Alan RuttenbergPERSON: Bjoern PetersPERSON: Larry HunterPERSON: Melanie Coutothas_specified_inputis_concretization_ofIs a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.replaced by: http://purl.obolibrary.org/obo/BFO_0000058PERSON: Alan RuttenburgPERSON: Barry Smithobsolete_is_concretization_oftrueis_specified_input_ofsome Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assayA relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.Alan RuttenbergPERSON:Bjoern Petersis_specified_input_ofis_concretized_asIs a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.replaced by: http://purl.obolibrary.org/obo/BFO_0000059PERSON: Alan RuttenbergPERSON: Barry Smithobsolete_is_concretized_astruehas_qualityA relation between an entity and a quality. For types: E has_quality Q iff:
for any eEt, exists qQt such that q inheres_in e at t.
For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm]replaced by: http://purl.obolibrary.org/obo/BFO_0000086GROUP:OBI:<http://obi.sourceforge.net>PERSON: Chris Mungallobsolete_has_qualitytruehas_specified_outputhas_specified_outputA relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.PERSON: Alan RuttenbergPERSON: Bjoern PetersPERSON: Larry HunterPERSON: Melanie Courtothas_specified_outputis_realized_byRelation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by'GROUP:OBI:<http://obi.sourceforge.net>PERSON: Chris Mungallexecuted_duringhas_realizationis_realized_asobsolete_is_realized_bytrueobsoleted_has_specified_output_informationA relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data.PERSON: Alan RuttenbergPERSON: Frank Gibsonobsoleted_has_specified_output_informationtrueis_manufactured_byhttp://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.Alan RuttenbergLiju Fanhas_makehas_manufactureris_manufactured_byhas_functionheart has_function to-pump-bloodRelation between an independent continuant and a function.replaced by: http://purl.obolibrary.org/obo/BFO_0000085GROUP:OBI:<http://obi.sourceforge.net>PERSON: Chris Mungallobsolete_has_functiontrueobsoleted_is_reagent_insome Triton X-100 (Sigma-Aldrich) is_reagent_in instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assayRelationship between a substance and a protocol application in which it participates, where the substance has a ReagentRoleAlan Ruttenbergobsoleted_is_reagent_intruerealizesexample of usage: The process of 'histidine catabolism' (GO:0006548) realizes the
function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity'
denotes a function and not a process). We leave open the possibility of defining
in future the sub-relations directly_realizes (as bewteen a function and it's
functioning) and indirectly_realizes.Relation between a process and a function, where the unfolding of the
process requires the execution of the function. Class level: P realizes F iff:
given any p that instantiates P, there exists some f, t such that f instantiates
F at t and p *realizes* f. Here, *realizes* is the primitive
instance level relation [GOC:cjm]replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes'GROUP:OBI:<http://obi.sourceforge.net>PERSON: Chris Mungalexecuteshas_function_partinvolves_execution_ofis_realization_ofobsolete_realizestrueobsoleted_utilizes_reagentsee example_of_usage for is_reagent_inRelationship between a protocol application and a substance that has role reagent that participates in the protocol applicationAlan Ruttenbergobsoleted_utilizes_reagenttrueobsoleted_is_device_forsome LKB 1272 Clinigamma counter is_device_for instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assayRelationship between a device and a protocol application in which it participatesAlan Ruttenbergobsoleted_is_device_fortrueis_specified_output_ofis_specified_output_ofA relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.Alan RuttenbergPERSON:Bjoern Petersis_specified_output_ofobsoleted_utilizes_devicesee example_of_usage for is_device_forRelationship between protocol application and an intrument in which it participatesAlan Ruttenbergobsoleted_utilizes_devicetrueis_proxy_forposition on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples:
A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality.
Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
level of radioactivity is_proxy_for level of toxicityA relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.A relation between continuant instances c1 and c2 where within a protocol
application, measurement of c1 is related to a what would be the
measurement of c2.
(another definition)Alan Ruttenbergis_proxy_forhas specified input informationA relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data.PERSON: Frank GibsonPERSON:Alan Ruttenbergconsumes dataobsoleted_has_specified_input_informationtruehas_roleA relation between a continuant C and a role R. The reciprocal relation of role_of.replaced by: http://purl.obolibrary.org/obo/BFO_0000087GROUP:OBI:<http://obi.sourceforge.net>PERSON:Chris Mungalobsolete_has_roletrueobsolete_results_from2009/11/23: BP, dev call:o bsoleted as discussed in tracker https://sourceforge.net/tracker/?func=detail&aid=2899860&group_id=177891&atid=886178
. Should be replaced by instead creating defined classes for materials, which are specified output of the process that conveys theobsolete_results_fromtrueachieves_planned_objectiveA cell sorting process achieves the objective specification 'material separation objective'This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.BP, AR, PPPB branchPPPB branch derivedmodified according to email thread from 1/23/09 in accordince with DT and PPPB branchachieves_planned_objectiveis_specified_information_output_ofA relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation.is replaced by has_specified_output_ofPERSON: James MaloneEditorobsoleted_is_specified_information_output_oftruehas grainthe relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard formPERSON: Alan RuttenbergPAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349has grainobsoleted_is_specified_information_intput_ofIs the inverse relation of has_specfied_input_informationis replaced by is_specified_intput_ofobsoleted_is_specified_information_intput_oftrueis grain ofA relation between granular parts and the whole of which they are a part. Granular parts have indeterminate number such that removing one granular part does not necessarily damage or diminish the whole.JAO: Added definition 2013-10-25 based on 'has grain', but both these terms seem problematic.PERSON: Alan RuttenbergDiscussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349is grain ofsuppliesA relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.GROUP: Relations branchsupplieshas_supplierA relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.PERSON: Alan RutternbergPERSON: Cristian CocosPERSON: Frank GibsonPERSON: Melanie Courtothas_supplierobjective_achieved_byThis relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.OBIOBIobjective_achieved_byis member of organizationRelating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a populationJZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.Person:Alan RuttenbergPerson:Helen ParkinsonPerson:Alan RuttenbergPerson:Helen Parkinson2009/09/28 Alan Ruttenberg. Fucoidan-use-caseis member of organizationhas category labelA relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale.has category labelhas disposition to bindA relationship between two material entitites that each have disposition to form a complex with the other. This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each otherIEDBhas disposition to bindhas organization memberRelating an organization to a legal person or organization.See tracker:
https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178Person: Jie Zhenghas organization memberspecifies value ofA relation between a value specification and an entity which the specification is about.specifies value ofhas value specificationA relation between an information content entity and a value specification that specifies its value.PERSON: James A. OvertonOBIhas value specificationhas performerperformer relation covers the need to report on who performed a planned processed. it has to cover processes done by People or Devices (such as a robot controlled by software WF management system)has performerprocess is result ofThe production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCRis a relationship between a process and a preceding occurrent that directly caused the later one to occurIEDBPERSON:Bjoern Petersprocess is result ofis_described_byobsolete_is_described_bytruebound_toA relationship between two material entities that form a complex based on a selective, non-covalent interaction.The definition of this term is modeled after the Chebi:50967 and GO:0005488 terms. Further alignment of the logical definitions with those ontologies will require agreement on the placement of GO:molecular function in BFO among other things. OBI will retire this term once such an alignment is achieved as 'bound to' is not in the primary OBI scope.bound_toinheres inthis fragility inheres in this vasethis red color inheres in this applea relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existenceA dependent inheres in its bearer at all times for which the dependent exists.inheres_ininheres inbearer ofthis apple is bearer of this red colorthis vase is bearer of this fragilitya relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existenceA bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.bearer_ofis bearer ofbearer ofparticipates inthis blood clot participates in this blood coagulationthis input material (or this output material) participates in this processthis investigator participates in this investigationa relation between a continuant and a process, in which the continuant is somehow involved in the processparticipates_inparticipates inhas participantthis blood coagulation has participant this blood clotthis investigation has participant this investigatorthis process has participant this input material (or this output material)a relation between a process and a continuant, in which the continuant is somehow involved in the processHas_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.has_participanthttp://www.obofoundry.org/ro/#OBO_REL:has_participanthas participantA journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.is concretized asA journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.concretizesthis catalysis function is a function of this enzymea relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existenceA function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.function_ofis function offunction ofthis red color is a quality of this applea relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existenceA quality inheres in its bearer at all times for which the quality exists.is quality ofquality_ofquality ofthis investigator role is a role of this persona relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existenceA role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.is role ofrole_ofrole ofthis enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existenceA bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.has_functionhas functionthis apple has quality this red colora relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existenceA bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.has_qualityhas qualitythis person has role this investigator role (more colloquially: this person has this role of investigator)a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existenceA bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.has_rolehas rolea relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existencehas dispositiondisposition ofderives fromthis cell derives from this parent cell (cell division)this nucleus derives from this parent nucleus (nuclear division)a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entityThis is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.derives_fromderives fromthis parent cell derives into this cell (cell division)this parent nucleus derives into this nucleus (nuclear division)a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entityThis is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.derives_intoderives intois location ofmy head is the location of my brainthis cage is the location of this rata relation between two independent continuants, the location and the target, in which the target is entirely within the locationMost location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTimelocation_oflocation oflocated inmy brain is located in my headthis rat is located in this cagea relation between two independent continuants, the target and the location, in which the target is entirely within the locationLocation as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterusMost location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTimelocated_inhttp://www.obofoundry.org/ro/#OBO_REL:located_inlocated inthe surface of my skin is a 2D boundary of my bodya relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entityA 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.2D_boundary_ofboundary ofis 2D boundary ofis boundary of2D boundary ofmy body has 2D boundary the surface of my skina relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entityA 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.has boundaryhas_2D_boundaryhas 2D boundaryDavid Osumi-Sutherlandstarts_at_end_ofX immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)immediately preceded byDavid Osumi-Sutherlandends_at_start_ofmeetsX immediately_precedes_Y iff: end(X) simultaneous_with start(Y)immediately precedessurrounded byx surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps ysurrounded byadjacent tomove to BFO?AllenA relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.temporal relationinverse of starts withChris MungallAllenstartsAn organism that is a member of a population of organismsis member of is a mereological relation between a item and a collection.is member ofmember part ofSIOmember ofhas member is a mereological relation between a collection and an item.SIOhas memberhas measurement valuehas x coordinate valuehas z coordinate valuehas y coordinate valuehas_feature_valuehas_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values.James Malonehas_feature_valuehas specified numeric valueA relation between a value specification and a number that quantifies it.A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.PERSON: James A. OvertonOBIhas specified numeric valuehas specified valueA relation between a value specification and a literal.This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.OBIhas specified valueentityEntityJulius CaesarVerdi’s Requiemthe Second World Waryour body mass indexBFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdfAn entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])entityEntity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdfper discussion with Barry SmithAn entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])continuantContinuantAn entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuantsA continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuantContinuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuantsA continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrentOccurrentAn entity that has temporal parts and that happens, unfolds or develops through time.BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial regionBFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrentOccurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.per discussion with Barry SmithSimons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] icIndependentContinuanta chaira hearta lega moleculea spatial regionan atoman orchestra.an organismthe bottom right portion of a human torsothe interior of your mouthA continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuantb is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.obsolete dependent continuanttrues-regionSpatialRegionBFO 2 Reference: Spatial regions do not participate in processes.Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial regionSpatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.per discussion with Barry SmithA spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] t-regionTemporalRegionTemporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensionalA temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensionalper discussion with Barry SmithA temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] 2d-s-regionTwoDimensionalSpatialRegionan infinitely thin plane in space.the surface of a sphere-shaped part of spaceA two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial regionA two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] st-regionSpatiotemporalRegionthe spatiotemporal region occupied by a human lifethe spatiotemporal region occupied by a process of cellular meiosis.the spatiotemporal region occupied by the development of a cancer tumorA spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])Every spatiotemporal region occupies_spatiotemporal_region itself.Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal regionA spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] processProcessa process of cell-division, \ a beating of the hearta process of meiosisa process of sleepingthe course of a diseasethe flight of a birdthe life of an organismyour process of aging.An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] processp is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] dispositionDispositionan atom of element X has the disposition to decay to an atom of element Ycertain people have a predisposition to colon cancerchildren are innately disposed to categorize objects in certain ways.the cell wall is disposed to filter chemicals in endocytosis and exocytosisBFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] dispositionb is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizableRealizableEntitythe disposition of this piece of metal to conduct electricity.the disposition of your blood to coagulatethe function of your reproductive organsthe role of being a doctorthe role of this boundary to delineate where Utah and Colorado meetA specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entityTo say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] 0d-s-regionZeroDimensionalSpatialRegionA zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial regionA zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] qualityQualitythe ambient temperature of this portion of airthe color of a tomatothe length of the circumference of your waistthe mass of this piece of gold.the shape of your nosethe shape of your nostrila quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] qualitya quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdcSpecificallyDependentContinuantReciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this keyof one-sided specifically dependent continuants: the mass of this tomatoof relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.the disposition of this fish to decaythe function of this heart: to pump bloodthe mutual dependence of proton donors and acceptors in chemical reactions [79the mutual dependence of the role predator and the role prey as played by two organisms in a given interactionthe pink color of a medium rare piece of grilled filet mignon at its centerthe role of being a doctorthe shape of this hole.the smell of this portion of mozzarellaA continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuantb is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.per discussion with Barry Smith(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] roleRoleJohn’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.the priest rolethe role of a boundary to demarcate two neighboring administrative territoriesthe role of a building in serving as a military targetthe role of a stone in marking a property boundarythe role of subject in a clinical trialthe student roleA realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] roleb is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-objectfiat-object-partFiatObjectPartor with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29the FMA:regional parts of an intact human body.the Western hemisphere of the Earththe division of the brain into regionsthe division of the planet into hemispheresthe dorsal and ventral surfaces of the bodythe upper and lower lobes of the left lungBFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisionsb is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat objectfiat object partb is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] 1d-s-regionOneDimensionalSpatialRegionan edge of a cube-shaped portion of space.A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial regionA one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] object-aggregateObjectAggregatea collection of cells in a blood biobank.a swarm of bees is an aggregate of members who are linked together through natural bondsa symphony orchestraan organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)defined by fiat: the aggregate of members of an organizationdefined through physical attachment: the aggregate of atoms in a lump of granitedefined through physical containment: the aggregate of molecules of carbon dioxide in a sealed containerdefined via attributive delimitations such as: the patients in this hospitalthe aggregate of bearings in a constant velocity axle jointthe aggregate of blood cells in your bodythe nitrogen atoms in the atmospherethe restaurants in Palo Altoyour collection of Meissen ceramic plates.An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregateAn entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] 3d-s-regionThreeDimensionalSpatialRegiona cube-shaped region of spacea sphere-shaped region of space,A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial regionA three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] siteSiteManhattan Canyon)a hole in the interior of a portion of cheesea rabbit holean air traffic control region defined in the airspace above an airportthe Grand Canyonthe Piazza San Marcothe cockpit of an aircraftthe hold of a shipthe interior of a kangaroo pouchthe interior of the trunk of your carthe interior of your bedroomthe interior of your officethe interior of your refrigeratorthe lumen of your gutyour left nostril (a fiat part – the opening – of your left nasal cavity)b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] siteb is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] objectObjectatomcellcells and organismsengineered artifactsgrain of sandmoleculeorganelleorganismplanetsolid portions of matterstarBFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47BFO 2 Reference: an object is a maximal causally unified material entityBFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])objectb is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])gdcGenericallyDependentContinuantThe entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.the pdf file on your laptop, the pdf file that is a copy thereof on my laptopthe sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuantb is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] functionFunctionthe function of a hammer to drive in nailsthe function of a heart pacemaker to regulate the beating of a heart through electricitythe function of amylase in saliva to break down starch into sugarBFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] functionA function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] p-boundaryProcessBoundarythe boundary between the 2nd and 3rd year of your life.p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundaryp is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] 1d-t-regionOneDimensionalTemporalRegionthe temporal region during which a process occurs.BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal regionA one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] materialMaterialEntitya flamea forest firea human beinga hurricanea photona puff of smokea sea wavea tornadoan aggregate of human beings.an energy wavean epidemicthe undetached arm of a human beingAn independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entityA material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] cf-boundaryContinuantFiatBoundaryb is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.Every continuant fiat boundary is located at some spatial region at every time at which it exists(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundaryb is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] immaterialImmaterialEntityBFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10immaterial entity1d-cf-boundaryOneDimensionalContinuantFiatBoundaryThe Equatorall geopolitical boundariesall lines of latitude and longitudethe line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.the median sulcus of your tonguea one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundarya one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] process-profileProcessProfileOn a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levelsOne important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profileb is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] r-qualityRelationalQualityJohn’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.a marriage bond, an instance of love, an obligation between one person and another.b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational qualityb is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 2d-cf-boundaryTwoDimensionalContinuantFiatBoundarya two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundarya two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] 0d-cf-boundaryZeroDimensionalContinuantFiatBoundarythe geographic North Polethe point of origin of some spatial coordinate system.the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meetzero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundaryzero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.requested by Melanie Courtota zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-t-regionZeroDimensionalTemporalRegiona temporal region that is occupied by a process boundaryright nowthe moment at which a child is bornthe moment at which a finger is detached in an industrial accidentthe moment of death.temporal instant.A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal regionA zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] historyHistoryA history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])historyA history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])waterAn oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms.waterATPAn adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways.ATPbiotinAn organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins.biotinpeptideAmide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.peptidedeoxyribonucleic acidHigh molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.deoxyribonucleic acidhydrogensulfiteA sulfur oxoanion that has formula HO3S.hydrogensulfiteglucoseAn aldohexose used as a source of energy and metabolic intermediate.glucose5'-adenylyl sulfateAn adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups.5'-adenylyl sulfatemolecular entityAny constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as wellmolecular entitycytochalasincytochalasinN-ethyl-N-nitrosoureaA member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups.N-ethyl-N-nitrosoureaprotonNuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.protonluciferinA low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase.luciferinsodium chlorideAn inorganic chloride salt having sodium(1+) as the counterion.sodium chloridelead(0)An elemental lead that has formula Pb.lead(0)acrylamideA member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia.acrylamidehydroxylAn oxygen radical that has formula HO.hydroxyldeuterium atomThe stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second).deuterium atomruthenium atomAn iron group element atom that has formula Ru.ruthenium atomfluoresceinA xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy.fluoresceingadodiamide hydrateThe hydrate of gadodiamide.gadodiamide hydrategadoteridolA non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI).gadoteridolphenol red3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney.phenol redsodium citrate dihydrateThe dihydrate of trisodium citrate.sodium citrate dihydrateatomA chemical entity constituting the smallest component of an element having the chemical properties of the element.atomrare earth metal atomrare earth metal atomrhodium atomA cobalt group element atom that has formula Rh.rhodium atomgadolinium atomA lanthanoid atom that has formula Gd.gadolinium atomterbium atomA lanthanoid atom that has formula Tb.terbium atomnucleic acidA macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.nucleic acidribonucleic acidHigh molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.ribonucleic acidamino acidA carboxylic acid containing one or more amino groups.amino acidmacromoleculeA macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.polymermacromoleculegadolinium molecular entitygadolinium molecular entitygadodiamideA non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI).gadodiamidesodium phosphatesodium phosphatephosphorus-32 atomThe radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.phosphorus-32 atomphosphorus-33 atomThe radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.phosphorus-33 atomCy3 dyeCy3 dyeCy5 dyeCy5 dyedigoxigeninA hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis.digoxigeninethylenediaminetetraacetic acidA polyamino carboxylic acid that has formula C10H16N2O8.ethylenediaminetetraacetic aciddouble-stranded DNAdouble-stranded DNA5-bromo-2'-deoxyuridineA pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase.5-bromo-2'-deoxyuridinechromium-51A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival.chromium-51Alexa Fluor 532An organosulfonic acid that has formula C34H33N3O11S2.Alexa Fluor 532Alexa Fluor 546An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3.Alexa Fluor 546Alexa Fluor 555A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate.Alexa Fluor 555tritiated thymidineThymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis.tritiated thymidinedimethyl sulfateThe dimethyl ester of sulfuric acid.dimethyl sulfatediethyl pyrocarbonateThe diethyl ester of dicarbonic acid.diethyl pyrocarbonate1,1-dihydroxy-3-ethoxy-2-butanoneA butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position.1,1-dihydroxy-3-ethoxy-2-butanoneN-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimideA carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents.N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimideN-methylisatoic anhydrideA 3,1-benzoxazin-1,4-dione having an N-methyl substituent.N-methylisatoic anhydride(S)-1-(4-bromoacetamidobenzyl)EDTAA tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration.(S)-1-(4-bromoacetamidobenzyl)EDTAEDTA methidiumpropylamideA combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe.EDTA methidiumpropylamidebromophenol blue3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye.bromophenol blueoxygen radicalAn inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species.oxygen radicaltrisA primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC.trisAny type of microscopy where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores.FMfluorescence imagingfluorescence microscopic imagingCHMOfluorescence microscopyMicroscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence.CLSMLSCMconfocal fluorescence imagingconfocal fluorescence microscopyconfocal laser scanning fluorescence microscopyconfocal laser scanning microscopyconfocal-laser scanning microscopyfluorescence confocal microscopyfluorescence confocal scanning laser microscopyscanning confocal fluorescence microscopyCHMOconfocal fluorescence microscopyMicroscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image.OMlight microscopyoptical microscopyCHMOlight microscopyA method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series.LC-MS-MSLC-MS/MSLC-MS2LC-MSMSLC/MS/MSLCMSMSliquid chromatography tandem mass spectrometryliquid chromatography tandem mass spectroscopyliquid chromatography-tandem mass spectroscopyCHMOliquid chromatography-tandem mass spectrometrycell line cellA cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in cultureA cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
cell line cell'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time.mortal cell line cellA cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence.mortal cell line cellimmortal cell line cellA cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.immortal cell line cellcell lineA cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
cell lineimmortal cell lineA cell line that is expected to be capable of indefinite propagation in an vitro culture.immortal cell line0mortal cell lineA cell line is able to support only a limited number of passages in vitro.mortal cell linecellcellPMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.cellcellprimary cultured cellA cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.primary cultured cellnative cellA cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).native cellcultured cellA cell in vitro that is or has been maintained or propagated as part of a cell culture.cultured cellfibroblastA connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.fibroblastepithelial cellA cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.epithelial cellT cellA type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.T cellmast cellA cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development.mast cellhepatocyteThe main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.hepatocyteerythrocyteA red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.erythrocytemacrophageA mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.macrophageB cellA lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.B celldendritic cellA cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).dendritic celllymphocyteA lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.lymphocyteexperimentally modified cell in vitroA cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.experimentally modified cell in vitroCD4-positive, alpha-beta T cellA mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor.CD4-positive, alpha-beta T cellCD8-positive, alpha-beta T cellA T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor.CD8-positive, alpha-beta T cellbasophilAny of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.basophilplasma cellA terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin.plasma cellalpha-beta T cellA T cell that expresses an alpha-beta T cell receptor complex.alpha-beta T cellCD8-positive, alpha-beta cytotoxic T cellA CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive.CD8-positive, alpha-beta cytotoxic T cellmature NK T cellA mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response.mature NK T cellmononuclear cellA leukocyte with a single non-segmented nucleus in the mature form.mononuclear cellsoilSoil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms.soilpodzolPodzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics.podzolenvironmental materialA portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.environmental materialgeographic locationA reference to a place on the Earth, by its name or by its geographical location.geographic locationcore promoter bindingInteracting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.core promoter bindingaction potentialA process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.action potentialantibody-dependent cellular cytotoxicityCytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells.antibody-dependent cellular cytotoxicitytype IV hypersensitivityAn inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation.type IV hypersensitivitycytokine productionThe appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.cytokine productioncell killingAny process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.cell killingT cell mediated cytotoxicityThe directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.T cell mediated cytotoxicityadaptive immune responseAn immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory).adaptive immune responsecytokine production involved in immune responseThe appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels.cytokine production involved in immune responseplatelet activating factor productionThe synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels.platelet activating factor productiontolerance inductionA process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it.tolerance inductionB cell tolerance inductionA process involving any mechanism for tolerance induction in B cells.B cell tolerance inductionT cell tolerance inductionA process involving any mechanism for tolerance induction in T cells.T cell tolerance inductionhypersensitivityAn inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system.hypersensitivitycytokine production involved in inflammatory responseThe synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels.cytokine production involved in inflammatory responsemolecular_functionElemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.molecular_functionantigen bindingInteracting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.antigen bindingcatalytic activityCatalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.catalytic activityRNA-directed DNA polymerase activityCatalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.RNA-directed DNA polymerase activityion channel activityCatalysis of facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.ion channel activitycellular_componentThe part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.cellular_componentchromosomeA structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.chromosomemitochondrionA semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.mitochondrionglucose metabolic processThe chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.glucose metabolic processDNA replicationThe cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.DNA replicationDNA methylationThe covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.DNA methylationchromatin remodelingDynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.chromatin remodelingphagocytosisAn endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.phagocytosisimmune responseAny immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.immune responsecellular response to DNA damage stimulusAny process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.cellular response to DNA damage stimuluscell cycleThe progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.cell cycleblood coagulationThe sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.blood coagulationbiological_processAny process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.biological_processopsonizationThe process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody.opsonizationcell proliferationThe multiplication or reproduction of cells, resulting in the expansion of a cell population.cell proliferationfertilizationThe union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).fertilizationcellular processAny process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.cellular processgene expressionThe process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.gene expressionvascular endothelial growth factor productionThe appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.vascular endothelial growth factor productionimmunoglobulin mediated immune responseAn immune response mediated by immunoglobulins, whether cell-bound or in solution.immunoglobulin mediated immune responsehistone modificationThe covalent alteration of one or more amino acid residues within a histone protein.histone modificationimmunoglobulin complexA protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.immunoglobulin complexB cell receptor complexAn immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.B cell receptor complexantigen processing and presentationThe process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.antigen processing and presentationprotein domain specific bindingInteracting selectively and non-covalently with a specific domain of a protein.protein domain specific bindingactin filament polymerizationAssembly of actin filaments by the addition of actin monomers to a filament.actin filament polymerizationhemopoiesisThe process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.hemopoiesisconnective tissue growth factor productionThe appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.connective tissue growth factor productionchemokine productionThe appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine productiongranulocyte macrophage colony-stimulating factor productionThe appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.granulocyte macrophage colony-stimulating factor productionhepatocyte growth factor productionThe appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.hepatocyte growth factor productiontype I interferon productionThe appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.type I interferon productioninterferon-beta productionThe appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interferon-beta productioninterferon-gamma productionThe appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon.interferon-gamma productioninterleukin-1 alpha productionThe appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-1 alpha productioninterleukin-1 beta productionThe appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-1 beta productioninterleukin-1 productionThe appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-1 productioninterleukin-10 productionThe appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-10 productioninterleukin-11 productionThe appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-11 productioninterleukin-12 productionThe appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-12 productioninterleukin-13 productionThe appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-13 productioninterleukin-14 productionThe appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-14 productioninterleukin-15 productionThe appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-15 productioninterleukin-16 productionThe appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-16 productioninterleukin-17 productionThe appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-17 productioninterleukin-18 productionThe appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-18 productioninterleukin-19 productionThe appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-19 productioninterleukin-2 productionThe appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-2 productioninterleukin-20 productionThe appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-20 productioninterleukin-21 productionThe appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-21 productioninterleukin-22 productionThe appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-22 productioninterleukin-23 productionThe appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-23 productioninterleukin-24 productionThe appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-24 productioninterleukin-25 productionThe appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-25 productioninterleukin-26 productionThe appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-26 productioninterleukin-27 productionThe appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-27 productioninterleukin-3 productionThe appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-3 productioninterleukin-4 productionThe appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-4 productioninterleukin-5 productionThe appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-5 productioninterleukin-6 productionThe appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-6 productioninterleukin-7 productionThe appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-7 productioninterleukin-8 productionThe appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-8 productioninterleukin-9 productionThe appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-9 productionTRAIL productionThe appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.TRAIL productiontumor necrosis factor productionThe appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.TNF alpha productiontumor necrosis factor productionlymphotoxin A productionThe appearance of lymphotoxin A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.TNF beta productionlymphotoxin A productiontransforming growth factor beta1 productionThe appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.transforming growth factor beta1 productiontransforming growth factor beta2 productionThe appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.transforming growth factor beta2 productiontransforming growth factor beta3 productionThe appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.transforming growth factor beta3 productionmacromolecule localizationAny process in which a macromolecule is transported to, or maintained in, a specific location.macromolecule localizationDNA polymerase activityCatalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.DNA polymerase activitytype III interferon productionThe appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon lambda is the only member of the type III interferon found so far.type III interferon productionchemokine (C-X-C motif) ligand 9 productionThe appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine (C-X-C motif) ligand 9 productionhelper T cell enhancement of adaptive immune responsePositive regulation of an adaptive immune response mediated via cytokine production by helper T cell.helper T cell enhancement of adaptive immune responsehelper T cell enhancement of T cell mediated immune responsePositive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell.helper T cell enhancement of T cell mediated immune responsehelper T cell enhancement of B cell mediated immune responsePositive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell.helper T cell enhancement of B cell mediated immune responsegranzyme A productionThe appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.granzyme A productionperforin productionThe appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.perforin productiongranulysin productionThe appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.granulysin productionchemokine (C-C motif) ligand 20 productionThe appearance of chemokine (C-C motif) ligand 20 (CCL20) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine (C-C motif) ligand 20 productionregulation of gene expression, epigeneticAny process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.regulation of gene expression, epigeneticregulation of molecular function, epigeneticAny heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya.regulation of molecular function, epigeneticT cell proliferationThe expansion of a T cell population by cell division. Follows T cell activation.T cell proliferationT cell receptor complexA protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.T cell receptor complexT cell activationThe change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.T cell activationimmunoglobulin complex, circulatingAn immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.antibodyantibodyimmunoglobulin complex, circulatingDNA polymerase complexA protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.DNA polymerase complexpeptide antigen bindingInteracting selectively and non-covalently with an antigen peptide.peptide antigen bindingMHC protein complexA transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.MHC protein complexmembrane-bounded organelleOrganized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.membrane-bounded organelleprotein complexA ribosome is a protein complexAny macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.protein complexcytotoxic T cell degranulationThe regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell.cytotoxic T cell degranulationsequence-specific DNA bindingInteracting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.sequence-specific DNA bindingregulation of DNA methylationAny process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.regulation of DNA methylationmacrophage migration inhibitory factor productionThe appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.macrophage migration inhibitory factor productionOncostatin M productionThe appearance of Oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.Oncostatin M productionchemokine (C-C motif) ligand 17 productionThe appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine (C-C motif) ligand 17 productioncellular developmental processA biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.cellular developmental processresponse to stimulusAny process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.response to stimuluschromosome organizationA process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.chromosome organizationactin polymerization-dependent cell motilityA process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell.actin polymerization-dependent cell motilitytransforming growth factor beta productionThe appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3.transforming growth factor beta productionmonocyte chemotactic protein-1 productionThe appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.monocyte chemotactic protein-1 productionchemokine (C-C motif) ligand 4 productionThe appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine (C-C motif) ligand 4 productionmacrophage inflammatory protein-1 gamma productionThe appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.macrophage inflammatory protein-1 gamma productionmacrophage inflammatory protein-1 alpha productionThe appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.macrophage inflammatory protein-1 alpha productionchemokine (C-C motif) ligand 5 productionThe appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine (C-C motif) ligand 5 productionchemokine (C-C motif) ligand 1 productionThe appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine (C-C motif) ligand 1 productiongranulocyte colony-stimulating factor productionThe appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.granulocyte colony-stimulating factor productionIP-10 productionThe appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.IP-10 productiongranzyme B productionThe appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.granzyme B productiontumor necrosis factor superfamily cytokine productionThe appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.tumor necrosis factor superfamily cytokine productionchemokine (C-C motif) ligand 22 productionThe appearance of chemokine (C-C motif) ligand 22 (CCL22) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine (C-C motif) ligand 22 productiontumor necrosis factor (ligand) superfamily member 11 productionThe appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.tumor necrosis factor (ligand) superfamily member 11 productioninterleukin-17A productionThe appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-17A productioninterleukin-17F productionThe appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.interleukin-17F productioncomplement-dependent cytotoxicityLysis of a cell resulting from triggering of the complement cascade. An example can be seen with complement activation and subsequent lysis of a bacterial cell as a result of the binding of IgM to the cell surface followed by the binding of complement proteins to that antibody.complement-dependent cytotoxicityhistamine secretion mediated by immunoglobulinHistamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface.histamine secretion mediated by immunoglobulinimmune complex formationThe process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus.immune complex formationimmunoglobulin-mediated neutralizationThe inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin.immunoglobulin-mediated neutralizationchemokine (C-C motif) ligand 19 productionThe appearance of chemokine (C-C motif) ligand 19 (CCL19) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine (C-C motif) ligand 19 productionchemokine (C-C motif) ligand 21 productionThe appearance of chemokine (C-C motif) ligand 21 (CCL21) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine (C-C motif) ligand 21 productionchemokine (C-X-C motif) ligand 12 productionThe appearance of chemokine (C-X-C motif) ligand 12 (CXCL12) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine (C-X-C motif) ligand 12 productionchemokine (C-X-C motif) ligand 13 productionThe appearance of chemokine (C-X-C motif) ligand 13 (CXCL13) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine (C-X-C motif) ligand 13 productionchemokine (C-X-C motif) ligand 16 productionThe appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.chemokine (C-X-C motif) ligand 16 productionneuron partAny constituent part of a neuron, the basic cellular unit of nervous tissue. A typical neuron consists of a cell body (often called the soma), an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.neuron partInsulin resistanceIncreased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels.Insulin resistanceconditional specificationa directive information entity that specifies what should happen if the trigger condition is fulfilledPlanAndPlannedProcess BranchOBI branch derivedOBI_0000349conditional specificationmeasurement unit labelExamples of measurement unit labels are liters, inches, weight per volume.A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.2009-03-16: provenance: a term measurement unit was
proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and
Cristian Cocos, and subsequently moved to IAO where the objective for
which the original term was defined was satisfied with the definition
of this, different, term.2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.PERSON: Alan RuttenbergPERSON: Melanie Courtotmeasurement unit labelobjective specificationIn the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.Answers the question, why did you do this experiment?PERSON: Alan RuttenbergPERSON: Barry SmithPERSON: Bjoern PetersPERSON: Jennifer Fostelgoal specificationOBI Plan and Planned Process/Roles BranchOBI_0000217objective specificationnarrative objectExamples of narrative objects are reports, journal articles, and patents submission.A narrative object is an information content entity that is a set of propositions.2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussionagree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositionsperson:Chris StoeckertOBI_0000013group:OBInarrative objectPour the contents of flask 1 into flask 2a directive information entity that describes an action the bearer will takeAlan RuttenbergOBI Plan and Planned Process branchaction specificationobsolete_artifacttruedatum labelA label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same labelhttp://www.golovchenko.org/cgi-bin/wnsearch?q=label#4nGROUP: IAO9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
datum labelsoftwareSoftware is a plan specification composed of a series of instructions that can be
interpreted by or directly executed by a processing unit.see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178PERSON: Alan RuttenbergPERSON: Bjoern PetersPERSON: Chris StoeckertPERSON: Melanie CourtotGROUP: OBIsoftwareobsolete_digital entityA digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
Superclass was 'digitial quality'person:Chris StoeckertOBI_0000261group:OBIobsolete2_digital entitytruejournal articleExamples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.a report that is published in a journalperson:Alan Ruttenbergperson:Chris StoeckertOBI_0000159group:OBIjournal articleinformation carrierIn the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.A quality of an information bearer that imparts the information content12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.PERSON: Alan RuttenbergSmith, Ceusters, Ruttenberg, 2000 years of philosophyinformation carriermodel numberA model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbersPerson: Alan Ruttenbergmodel numberobsolete_material_entitytruebinary digital entityMS Word document, ZIP file, DICOM file, JPEG fileA binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
Superclass was 'digital entity'digital_entityperson:Chris StoeckertOBI_0000244group:OBIobsolete2_binary digital entitytrueThe length of a ruler.a unit of measure is the quality of some material entity compared to which another quality is some multiple of.Alan RuttenbergSmith, Ceusters, Ruttenberg, 2000 years of philosophyobsolete_unit of measuretrueprogramming languageR, Perl, JavaA language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.person:Alan Ruttenbergperson:Chris StoeckertOBI_0000058group:OBIprogramming languagedata itemData items include counts of things, analyte concentrations, and statistical summaries.a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate beliefPERSON: Alan RuttenbergPERSON: Chris StoeckertPERSON: Jonathan Reesdatadata itemsymbola serial number such as "12324X"a stop signa written proper name such as "OBI"An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.20091104, MC: this needs work and will most probably change2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).PERSON: James A. OvertonPERSON: Jonathan Reesbased on Oxford English DictionarysymbolnumeralA symbol that denotes a number.PERSON: Jonathan Reesnumeralinformation content entityExamples of information content entites include journal articles, data, graphical layouts, and graphs.A generically dependent continuant that is about some thing.2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.PERSON: Chris StoeckertOBI_0000142information content entityinteger numerala numeral that denotes an integerPERSON: Jonathan Reesinteger numeral1110 feet. 3 ml.a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
this case we explicitly refer to the singular formWould write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.PERSON: Alan RuttenbergPERSON: Melanie Courtotscalar measurement datumAn information content entity whose concretizations indicate to their bearer how to realize them in a process.2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBOWerner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -AlanPERSON: Alan RuttenbergPERSON: Bjoern Petersdirective information entitytime triggerrevisit?PlanAndPlannedProcess BranchOBI branch derivedOBI_0000331time triggerobsolete_study interpretationA study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.Lawrence HunterPERSON: Alan RuttenbergPERSON: Jennifer FostelPERSON: Melanie CourtotconclusionOBI_0000005obsolete_study interpretationtruedot plotDot plot of SSC-H and FSC-H.A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.person:Allyson Listerperson:Chris StoeckertOBI_0000123group:OBIdot plotgraphA diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.PERSON: Lawrence Hunterperson:Alan Ruttenbergperson:Allyson ListerOBI_0000240group:OBIgraphtext based digital entityXML file, C++ source code fileA text based digital entity is a digital entity that is encoded so that it only contains text characters.3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
superclass was 'digital document'digital_entityperson:Chris StoeckertOBI_0000132group:OBIobsolete2_text based digital entitytrueruleexample to be addeda rule is an executable which guides, defines, restricts actionsMSIPRSOBI_0500021PRSrulecontour plotContour plot of SSC-H, FSC-H, and FL1-H.generically_dependent_continuantsperson:Allyson Listerperson:Chris StoeckertOBI_0000246group:Flow Cytometry communitycontour plotreport figureA report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elementsI prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some reportReplaced by defined version of figureperson:Alan Ruttenbergperson:Allyson ListerOBI_0000027group:OBIobsolete2_report figuretruealgorithmPMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.Philippe Rocca-SerraPlanAndPlannedProcess BranchOBI_0000270adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)algorithmsoftware interpreterR program, Perl interpreter, Java virtual machineA software interpreter is a software application that executes some specified input software. Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreterperson:Alan Ruttenbergperson:Chris StoeckertOBI_0000199group:OBIsoftware interpretercuration status specificationThe curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)PERSON:Bill BugGROUP:OBI:<http://purl.obolibrary.org/obo/obi>OBI_0000266curation status specificationdensity plotDensity plot of SSC-H and FSC-H.A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.person:Allyson Listerperson:Chris StoeckertOBI_0000179group:Flow Cytometry communitydensity plotreportExamples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on
something that has completed." Should it be restricted to those things
that are completed? For example, a progress report is (usually) about
something that definitely has *not* been completed, or may include
(only) projections. I think the definition would not suffer if the
whole sentence is deleted.2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussiondisagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarificationPERSON: Alan RuttenbergPERSON: Melanie CourtotPERSON:Chris StoeckertGROUP: OBIOBI_0000099reportreport elementA report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).2009-03-16: needs some more work (clarify relations).2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussionReplaced by textual entity and figureThere will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the textPERSON: Alan RuttenbergPERSON: Allyson ListerPERSON: Melanie CourtotGROUP:OBIOBI_0000001obsolete_report elementtruebinary executableBinary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
superclass was 'digital entity'person:Jennifer FostelOBI_0000222group:OBIobsolete2_binary executabletruesource code moduleThe written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.A source code module is a directive information entity that specifies, using a programming language, some algorithm.person:Alan Ruttenbergperson:Chris StoeckertOBI_0000039group:OBIsource code modulereport tableA report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussionperson:Alan Ruttenbergperson:Allyson ListerOBI_0000265group:OBIobsolete_report tabletruedata format specificationA data format specification is the information content borne by the document published defining the specification.
Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes
information. Example: The ISO document specifying what encompasses an
XML document; The instructions in a XSD file"PERSON: Alan RuttenbergPlanAndPlannedProcess BranchOBI branch derivedOBI_0000187data format specificationdata setIntensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.person:Allyson Listerperson:Chris StoeckertOBI_0000042group:OBIdata setimageAn image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.person:Alan Ruttenbergperson:Allysonperson:Chris StoeckertOBI_0000030group:OBIimagedata about an ontology part is a data item about a part of an ontology, for example a termPerson:Alan Ruttenbergdata about an ontology partplan specificationPMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.2014-03-31: A plan specification can have other parts, such as conditional specifications.Alternative previous definition: a plan is a set of instructions that specify how an objective should be achievedAlan RuttenbergOBI Plan and Planned Process branchOBI_00003442/3/2009 Comment from OBI review.
Action specification not well enough specified.
Conditional specification not well enough specified.
Question whether all plan specifications have objective specifications.
Request that IAO either clarify these or change definitions not to use themplan specificationdigital documentA digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
superclass was 'digial entity'person:Jennifer FostelOBI_0000195group:OBIobsolete2_digital documenttruemeasurement datumExamples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.2/2/2009 is_specified_output of some assay?person:Chris StoeckertOBI_0000305group:OBImeasurement datum_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.obsolete_identifiertrueversion numberA version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence versionGROUP: IAOversion numberserial numberA serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)GROUP: IAOserial numberlot numberA lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.GROUP: IAObatch numberlot numberA settings datum is a datum that denotes some configuration of an instrument.2/3/2009 Feedback from OBI
This should be a "setting specification". There is a question of whether it is information about a realizable or not.
Pro other specification are about realizables.
Cons sometimes specifies a quality which is not a realizable.Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.setting datum3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4Need to rework digital entity. Digital quality was suggested by Barry.obsolete_digital qualitytrueconclusion textual entitythat fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.2009/09/28 Alan Ruttenberg. Fucoidan-use-case2009/10/23 Alan Ruttenberg: We need to work on the definition stillPerson:Alan Ruttenbergconclusion textual entitymaterial information bearerA page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.a braina hard driveA material entity in which a concretization of an information content entity inheres.GROUP: IAOmaterial information bearerhistogramA histogram is a report graph which is a statistical description of a
distribution in terms of occurrence frequencies of different event classes.PERSON:Chris StoeckertPERSON:James MalonePERSON:Melanie CourtotGROUP:OBIhistogramheatmapA heatmap is a report graph which is a graphical representation of data
where the values taken by a variable(s) are shown as colors in a
two-dimensional map.PERSON:Chris StoeckertPERSON:James MalonePERSON:Melanie CourtotGROUP:OBIheatmapVenn diagramA Venn diagram is a report graph showing all hypothetically possible
logical relations between a finite collection of sets.PERSON:Chris StoeckertPERSON:James MalonePERSON:Melanie CourtotWEB: http://en.wikipedia.org/wiki/Venn_diagramVenn diagramobsolete_survival curveA survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.PERSON:Chris StoeckertPERSON:James MalonePERSON:Melanie CourtotWEB: http://www.graphpad.com/www/book/survive.htmobsolete_survival curvetruedendrogramDendrograms are often used in computational biology to
illustrate the clustering of genes.A dendrogram is a report graph which is a tree diagram
frequently used to illustrate the arrangement of the clusters produced by a
clustering algorithm.PERSON:Chris StoeckertPERSON:James MalonePERSON:Melanie CourtotWEB: http://en.wikipedia.org/wiki/Dendrogramdendrogramscatter plotComparison of gene expression values in two samples can be displayed in a scatter plotA scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.PERSON:Chris StoeckertPERSON:James MalonePERSON:Melanie CourtotscattergraphWEB: http://en.wikipedia.org/wiki/Scatterplotscatter plotA photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.PERSON:Alan RuttenbergPERSON:Joanne LucianoPERSON:Melanie CourtotWEB: http://en.wiktionary.org/wiki/photographphotographphotographic printA photographic print is a material entity upon which a photograph generically depends.PERSON:Alan RuttenbergPERSON:Melanie Courtotphotographic printobsolescence reason specificationThe reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.PERSON: Alan RuttenbergPERSON: Melanie Courtotobsolescence reason specificationtextual entityWords, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entitiesA textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.PERSON: Lawrence Huntertexttextual entitycitationVerspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.a textual entity intended to identify a particular publicationPERSON: Lawrence Huntercitationauthor identificationL. HunterA textual entity intended to identify a particular authorPERSON: Lawrence Hunterauthor identificationinstitutional identificationUniversity of Colorado Denver School of MedicineA textual entity intended to identify a particular institutionPERSON: Lawrence Hunterinstitutional identificationcaptionFigure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.A textual entity that describes a figurePERSON: Lawrence Huntercaptiondocument titleTextual characteristics of traditional and Open Access scientific journals are similarA textual entity that names a documentPERSON: Lawrence Hunterdocument titletable| T F
--+-----
T | T F
F | F FA textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositionsPERSON: Lawrence Huntertabletable of abbreviationsIAO information artifact ontology
OBI ontology of biomedical investiations
GO gene ontologyA table where the constituent texts are abbreviations and their expansionsPERSON: Lawrence Huntertable of abbreviationsfigureAny picture, diagram or tableAn information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.PERSON: Lawrence HunterfigurediagramA molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.A figure that expresses one or more propositionsPERSON: Lawrence HunterdiagramdocumentA journal article, patent application, laboratory notebook, or a bookA collection of information content entities intended to be understood together as a wholePERSON: Lawrence HunterdocumentpublicationA journal article or bookA document that has been accepted by a publisherPERSON: Lawrence Hunterpublicationpublication about an investigationMost scientific journal articlesA publication that is about an investigationPERSON: Lawrence Hunterscientific publicationpublication about an investigationpatentUS Patent 6,449,603A document that has been accepted by a patent authorityPERSON: Lawrence Hunterpatentdocument partAn abstract, introduction, method or results section.an information content entity that is part of a documentPERSON: Lawrence Hunterdocument partabstractThe profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.PERSON: Lawrence Hunterabstractintroduction to a publication about an investigationSection labelled 'introduction' of a typical scientific journal articleA part of a publication about an investigation that is about the objective specification (why the investigation is being done)PERSON: Lawrence Hunterbackgroundintroductionintroduction to a publication about an investigationmethods sectionThe section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.A part of a publication about an investigation that is about the study design of the investigationPERSON: Lawrence Hunterexperimentalexperimental proceduresexperimental sectionmethodsmethods sectionresults sectionThe section labelled 'results' in a typical scientific journal articleA part of a publication about an investigation that is about a study design executionPERSON: Lawrence Hunterresultsresults sectiondiscussion section of a publication about an investigationA part of a publication about an investigation that is about the study interpretation of the investigationPERSON: Lawrence Hunterdiscussiondiscussion sectiondiscussion section of a publication about an investigationreferences sectionThe list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"A part of a document that has citations as partsPERSON: Lawrence Hunterreferences sectionauthor listLawrence Hunter and Kevin Brettonel Cohenpart of a document that enumerates the authors of the documentPERSON: Lawrence Hunterauthor listinstitution listThe University of Colorado Denver School of Medicine and the University of Colorado Boulder.part of a document that has parts that are institution identifications associated with the authors of the documentPERSON: Lawrence Hunterinstitution listauthor contributions sectionLH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.A part of a publication that is about the specific contributions of each authorPERSON: Lawrence Hunterauthor contributionscontributions by the authorsauthor contributions sectionacknowledgements sectionThe authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscriptPart of a publication that is about the contributions of people or institutions other than the authors.PERSON: Lawrence Hunteracknowledgementsacknowledgmentsacknowledgements sectionfootnoteThe referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.PERSON: Lawrence Hunterendnotefootnotesupplementary material to a documentpart of a document that is segregated from the rest of the document due to its sizePERSON: Lawrence Hunteradditional informationappendixsupplemental informationsupplementary materialsupporting informationsupplementary material to a documenttable of contentsA table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).PERSON: Lawrence Huntertable of contentstable of figuresA table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).PERSON: Lawrence Huntertable of figuresrunning titleA shorter version of a document titlePERSON: Lawrence Hunterrunning titlecopyright sectionThis work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.A document part that describes legal restrictions on making or distributing copies of the documentPERSON: Lawrence Huntercopyright section1A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617Alan RuttenbergAR notes: We need to discuss whether it should include site.cartesian spatial coordinate datumhttp://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb6171A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial regionAlan Ruttenbergone dimensional cartesian spatial coordinate datum11A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial regionAlan Ruttenbergtwo dimensional cartesian spatial coordinate datum111A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial regionAlan Ruttenbergthree dimensional cartesian spatial coordinate datumA scalar measurement datum that is the result of measurement of length qualityAlan Ruttenberglength measurement datumThe Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.A denotator type indicates how a term should be interpreted from an ontological perspective.Alan RuttenbergBarry Smith, Werner Ceustersdenotator typeA scalar measurement datum that is the result of measurement of mass quality2009/09/28 Alan Ruttenberg. Fucoidan-use-casePerson:Alan Ruttenbergmass measurement datumhypothesis textual entitythat fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660A textual entity that expresses an assertion that is intended to be tested.2009/09/28 Alan Ruttenberg. Fucoidan-use-casePerson:Alan Ruttenberghypothesis textual entityA scalar measurement datum that is the result of measuring a temporal interval2009/09/28 Alan Ruttenberg. Fucoidan-use-casePerson:Alan Ruttenbergtime measurement datumA textual entity that is used as directive to deliver something to a person, or organization2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59postal addressemail addressAlan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583Person:Alan RuttenbergPerson:Chris Stoeckartemail addressauthor roleA role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.PERSON: Alan RuttenbergPERSON: Melanie Courtotauthor rolea planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexingPerson:Alan Ruttenbergdata item extraction from journal articleRecording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.a planned process in which a document is created or added to by including the specified input in it.6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tapeBjoern Peterswikipedia http://en.wikipedia.org/wiki/Documentingdocumentingline graphA line graph is a type of graph created by connecting a series of data
points together with a line.PERSON:Chris StoeckertPERSON:Melanie Courtotline chartGROUP:OBIWEB: http://en.wikipedia.org/wiki/Line_chartline graphA new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.Person:Alan RuttenbergPerson:Bjoern PetersPerson:Melanie Courtotassigning a CRIDassigning a centrally registered identifierArticles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. A planned process in which a CRID registry associates an information content entity with a CRID symbolPERSON:Alan Ruttenbergassociating information with a CRID in the CRID registryassociating information with a centrally registered identifier in its registrya planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.obsolete_establishing a CRID registrytrueThe sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.PERSON: Alan RuttenbergPERSON: Bill HoganPERSON: Bjoern PetersPERSON: Melanie CourtotCRID symbolOriginal proposal from Bjoern, discussions at IAO callscentrally registered identifier symbolThe sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.PERSON: Alan RuttenbergPERSON: Bill HoganPERSON: Bjoern PetersPERSON: Melanie CourtotCRIDOriginal proposal from Bjoern, discussions at IAO callscentrally registered identifierPubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.PERSON: Alan RuttenbergPERSON: Bill HoganPERSON: Bjoern PetersPERSON: Melanie CourtotCRID registryOriginal proposal from Bjoern, discussions at IAO callscentrally registered identifier registryGoing to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbolPERSON: Alan RuttenbergPERSON: Bill HoganPERSON: Bjoern PetersPERSON: Melanie Courtotlooking up a CRIDlooking up a centrally registered identifiertime stamped measurement datumpmid:20604925 - time-lapse live cell microscopyA data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.Alan Ruttenbergexperimental time seriestime sampled measurement data setwritten name"Bill Clinton""The Eiffel Tower""United States of America"A textual entity that denotes a particular in reality.PERSON: Bill Hoganhttps://github.com/information-artifact-ontology/IAO/issues/114The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.written nameA software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.PERSON: Melanie CourtotPERSON: Michel Dumontierhttps://github.com/information-artifact-ontology/IAO/issues/80software method A software module is software composed of a collection of software methods.PERSON: Melanei CourtotPERSON: Michel Dumontierhttps://github.com/information-artifact-ontology/IAO/issues/80software moduleA software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.PERSON: Melanie CourtotPERSON: Michel Dumontierhttps://github.com/information-artifact-ontology/IAO/issues/80software libraryA software application is software that can be directly executed by some processing unit.PERSON: Melanie CourtotPERSON: Michel Dumontierhttps://github.com/information-artifact-ontology/IAO/issues/80software application A software script is software whose instructions can be executed using a software
interpreter.PERSON: Melanie CourtotPERSON: Michel Dumontierhttps://github.com/information-artifact-ontology/IAO/issues/80software scriptabbreviation textual entityFrom Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):
BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect.A textual entity listing abbreviations and their expansions that are used in a document.PERSON: Bill Baumgartnerabbreviation textual entityabbreviations sectionThe section labelled 'abbreviations' in a typical scientific journal article.A part of a document where abbreviations and their long-forms used within the document are listed.PERSON: Bill Baumgartnerabbreviationsabbreviations listabbreviations usedlist of abbreviationslist of abbreviations usedabbreviations sectionauthor information sectionThe section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.PERSON: Bill Baumgartnerauthor informationauthors’ informationauthor information sectionauthor information textual entityFrom Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/):
IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.PERSON: Bill Baumgartnerauthor information textual entityauthor summary sectionThe section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers.PERSON: Bill Baumgartnerauthor summarysummarysynopsisArticle submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)author summary sectionauthor summary textual entityFrom Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/):
The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX.A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).PERSON: Bill BaumgartnerArticle submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).author summary textual entityavailability sectionThe section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained.PERSON: Bill Baumgartneravailabilityavailability sectionavailability textual entityFrom Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):
Project home page:http://krux.googlecode.comA textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.PERSON: Bill Baumgartneravailability textual entitycase report sectionThe section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)A part of a document about the medical history of a specific patient as it relates to the topic of the document.PERSON: Bill Baumgartnercase presentationcase reportcase report sectioncase report textual entityExcerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/):
The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.PERSON: Bill Baumgartnercase report textual entityconclusion sectionThe section labelled 'conclusion' in a typical scientific journal article.A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. PERSON: Bill Baumgartnerconcluding remarksconclusionconclusionsfindingssummaryconclusion sectionconflict of interest sectionThe section labelled 'conflict of interest statement' in a typical scientific journal article.A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document.PERSON: Bill Baumgartnercompeting interestsconflict of interestconflict of interest statementdeclaration of competing interestsdisclosure of potential conflicts of interestconflict of interest sectionconflict of interest statementSD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document.PERSON: Bill Baumgartnerconflict of interest textual entityconsent sectionThe section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)A part of a document about the consent process that was used to enroll patients in a study.PERSON: Bill Baumgartnerconsentconsent sectionconsent textual entityFrom Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):
Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal.A textual entity that documents the consenting process used to enroll patients in a study.PERSON: Bill Baumgartnerconsent textual entityethical approval sectionThe section labelled 'ethical approval' in a typical scientific journal article.A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.PERSON: Bill Baumgartnerethical approvalethical approval sectionethical approval textual entityFrom McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):
The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review.A textual entity that documents the ethical approval of some study design.PERSON: Bill Baumgartnerethical approval textual entityfigures sectionThe section labelled 'figures' in a typical scientific journal article.A part of a document that contains one or more figures.PERSON: Bill Baumgartnerfiguresfigures sectionfunding source declaration sectionThe section labelled 'funding' in a typical scientific journal article.A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.PERSON: Bill Baumgartnerfundingfunding informationfunding sourcesfunding statementfunding/supportsource of fundingsources of fundingfunding source declaration sectionfunding souce declaration textual entityFrom Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/):
This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication.A textual entity documenting the source of funding that supported some study.PERSON: Bill Baumgartnerfunding source declaration textual entityfuture directions sectionThe section labelled 'future directions' in a typical scientific journal article.A part of a document detailing extensions of the described work that may be implemented at some future point in time.PERSON: Bill Baumgartnerfuture challengesfuture considerationsfuture developmentsfuture directionsfuture outlookfuture perspectivesfuture plansfuture prospectsfuture researchfuture research directionsfuture studiesfuture workfuture directions sectionfuture directions textual entityExcerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/):
In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members.A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.PERSON: Bill Baumgartnerfuture directions textual entitygenome announcement sectionThe section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)A document part announcing the publication of a novel draft genome sequence.PERSON: Bill Baumgartnergenome announcementgenome announcement sectiongenome announcement textual entityExcerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/):
Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB).A textual entity that describes the generation and public release of a novel, draft genome sequence.PERSON: Bill Baumgartnergenome announcement textual entitykeyword textual entityFrom: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/):
Exon orthology; alternative splicing; exon duplication; intron-exon structure.A textual entity listing keywords indicating the major theme(s) of a document.PERSON: Bill Baumgartnerkeyword textual entitykeywords sectionThe section labelled 'keywords' in a typical scientific journal article.A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.PERSON: Bill Baumgartnerkeywordskeywords sectionstudy limitations sectionThe section labelled 'limitations' in a typical scientific journal article.A part of a document about biases or short comings related to the study design and execution.PERSON: Bill Baumgartnerlimitationsstudy limitationsAuthor guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)study limitations sectionstudy limitations textual entityExcerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/).
Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out.A textual entity addressing a shortcoming or bias of a study design or execution.PERSON: Bill BaumgartnerAuthor guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)study limitations textual entitymaterials sectionThe section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)A part of a document about the materials required to reproduce the content of the document.PERSON: Bill Baumgartnermaterialsmaterials sectionnotes sectionThe section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.PERSON: Bill Baumgartnerfootnotesnotesnotes sectionpatients sectionThe section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)A part of a document about the patients that participated in a study.PERSON: Bill Baumgartnerpatients sectionpatients textual entityExcerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/):
Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred.A textual entity expressing information regarding the patients used in a study.PERSON: Bill Baumgartnerpatients textual entitypre-publication history sectionThe section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors.PERSON: Bill Baumgartnernotice of republicationpre-publication historypre-publication history sectionpre-publication history textual entityFrom Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/):
The pre-publication history for this paper can be accessed here:
http://www.biomedcentral.com/1471-2253/13/33/prepubA textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information.PERSON: Bill Baumgartnerpre-publication history textual entityrelated work sectionThe section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)A part of a document about work in other publications that is relevant to the content of the document.PERSON: Bill Baumgartnerrelated literaturerelated workrelated work sectionrelated work textual entityExcerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/):
Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).
A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.PERSON: Bill Baumgartnerrelated work textual entityrequirements sectionThe section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.PERSON: Bill Baumgartnerrequirementsrequirements sectionrequirements textual entityFrom Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):
• Operating systems: Platform independent
• Programming language: Matlab, R, Python
• Other requirements: None
• License: GNU GPL v3
• Any restrictions to use by non-academics: NoneA textual entity that expresses the requirements necessary to use a resource, e.g. software.PERSON: Bill Baumgartnerrequirements textual entitystatistical analysis textual entityFrom Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/):
Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant.A textual entity documenting statistical analysis tools and techniques employed.PERSON: Bill Baumgartnerstatistical analysis textual entitystatistical analysis sectionThe section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)A part of the document used to describe the statistical methodologies employed in the work presented in the document.PERSON: Bill Baumgartnerstatistical analysisstatistical analysis sectiontables sectionThe section labelled 'tables' in a typical scientific journal article.A part of a document that contains one or more tables.PERSON: Bill Baumgartnertablestables sectiondatabase extract, transform, and load processA planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the secondAlan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output.PERSON:Alan RuttenbergETLWEB:https://en.wikipedia.org/wiki/Extract,_transform,_loaddatabase extract, transform, and load processinfectionA part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population.infectionhuman pathogenicity dispositionA disposition to initiate processes that result in a disorder in a human organism.human pathogenicity dispositionMus musculushouse mousemouseMus musculusRattus norvegicusNorway ratRattus sp. strain Wistarbrown ratratratsRattus norvegicusVirusesVirusesHerpesviridaeHerpesviridaeCytomegalovirusCytomegalovirusHuman gammaherpesvirus 4Epstein Barr virusEpstein-Barr virusHuman gammaherpesvirus 4Hepatitis B virusHepatitis B virusHepatitis C virusHepatitis C virusPrimate lentivirus groupPrimate lentivirus groupHuman immunodeficiency virus 1Human immunodeficiency virus 1Human immunodeficiency virus 2Human immunodeficiency virus 2Euteleostomibony vertebratesEuteleostomiEcdysozoaEcdysozoaTreponema pallidumTreponema pallidumPancrustaceaPancrustaceaBacteriaeubacteriaBacteriaArchaeaArchaeaEukaryotaeucaryoteseukaryotesEukaryotaEuarchontogliresEuarchontogliresTetrapodatetrapodsTetrapodaAmniotaamniotesAmniotaOpisthokontaOpisthokontaBilateriaBilateriaRetro-transcribing virusesRetro-transcribing virusesArabidopsis thalianamouse-ear cressthale cressthale-cressArabidopsis thalianaHIV-1 group OHIV-1 group OMurinaeMurinaeMammaliamammalsMammaliaDictyostelium discoideumDictyostelium discoideumAscomycotaascomycetessac fungiAscomycotaSchizosaccharomyces pombefission yeastSchizosaccharomyces pombeSaccharomyces cerevisiaebaker's yeastbrewer's yeastlager beer yeastyeastSaccharomyces cerevisiaeNeurosporaNeurosporaCaenorhabditis elegansroundwormCaenorhabditis elegansDaphniacommon water fleasDaphniasaccharomycetasaccharomycetaDrosophila melanogasterfruit flyDrosophila melanogasterVertebrata <Metazoa>VertebratavertebratesVertebrata <Metazoa>Danio rerioleopard daniozebra daniozebra fishzebrafishDanio rerioXenopus <genus>XenopusXenopus <genus>Gallus gallusbantamchickenchickensGallus gallusHomo sapienshumanhuman beingmanHomo sapiensRodentiarodentRodentiarole of being consumer safety officerConsumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htmPerson charged with serving as CSO, FDA official who coordinates the reviewthe role of a human being that is realized by enforcing regulations to ensure consumer safetyJennifer FostelPerson:Helen ParkinsonOBI, CDISCrole of being consumer safety officerfluorescent reporter intensityA measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.person:Chris Stoeckertgroup:OBIFrom the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem.fluorescent reporter intensityplanned processplanned processInjecting mice with a vaccine in order to test its efficacyA processual entity that realizes a plan which is the concretization of a plan specification.'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some
objectives is a planned process.Bjoern Petersbranch derived6/11/9: Edited at workshop. Used to include: is initiated by an agentThis class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)planned processregulator roleFact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805a regulatory role involved with making and/or enforcing relevant legislation and governmental ordersPerson:Jennifer FostelregulatorOBIregulator rolebiological feature identification objectiveBiological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.Jennifer Fostelbiological feature identification objectiveregulation-assigned roleApproval letterRegulation-assigned role is a regulatory role defined by legislation or governmental ordersPerson: Jennifer Fostelregulation-assigned roleregulatory roleRegulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.GROUP: Role branchOBI, CDISCgovt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competentregulatory rolematerial supplier roleJackson Labs is an organization which provide mice as experimental materiala role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.Supplier role is a special kind of service, e.g. biobankPERSON:Jennifer Fostelmaterial provider rolesuppliermaterial supplier rolecontract research organization rolea worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study executionPerson: Jennifer Fostelcontract research organizationcontract research organization rolelist-mode data fileAn example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used.A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter.One example of usage is in the context of flow cytometry, however is not restricted to this community and is more widely used, e.g. by imaging people.person:Chris Stoeckertgroup:Flow Cytometry communitylist-mode data fileclassified data setA data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.PERSON: James MalonePERSON: Monnie McGeedata set with assigned class labelsclassified data setreference substance roleCalibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.htmla role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.Person:Jennifer Fostelreference substanceOBIreference substance rolecytological stain rolehaemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/HaematoxylinA dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualizationPerson:Helen ParkinsonPerson:Jennifer Fostelcytological staincytological stain rolecentrifuge pellet roleDefinition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pelletpellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material..GROUP: Role branchOBI9Mar09 after discussion with process branch changed definition to include use of centrifuge;centrifuge pellet roleclinical research coordinator rolea worker role comprised of handling the administrative duties of a trial or study.Person:Jennifer Fostelclinical research coordinatorclinical research coordinator rolesupernatant rolePrecipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipediasupernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material.GROUP: Role branchOBIsupernatant rolechromatography columnChromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms.Frank Gibsonhttp://en.wikipedia.org/wiki/Column_chromatographyopen tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178chromatography columndrug rolehttp://www.answers.com/topic/drug
1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication.
2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act.a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organismRole BranchdrugOBI, CDISCdrug rolepump valve switchA pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow.FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrumentOBI Instrument branchOBIpump valve switchxenotransplantationis the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humansPlanAndPlannedProcess BranchOBI branch derivedxenotransplantationphysical documenta book is a physical documentA physical document is an object serving as a record of information by means of symbolic marks.PERSON: Bjoern PetersGROUP: OBIphysical documentwaitingnot actively doing anything to a material for a duration of time.PERSON:Alan RuttenbergOBI branch derivedBP: I have doubts about the utility of this.We need a better handling/modeling of time (January 2008)waitingprocessed materialExamples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samplesIs a material entity that is created or changed during material processing.PERSON: Alan Ruttenbergprocessed materialchromatography devicea device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.Frank Gibsonchromatography instrumenthttp://en.wikipedia.org/wiki/Chromatographyopen tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178chromatography devicemass spectrometerLCQ Fleet Ion Trap MSn manufactured by thermo fisher scientificA mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrumFrank Gibsonhttp://en.wikipedia.org/wiki/Mass_spectrometrymass spectrometerplatformA platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI.OBI Instrument branchOBI Instrument branchrem1: We decided at the Philly workshop that consumables do not include reagents.
FG: we could actully add a relation to platform which would be "has_part some instrument"
DS: Sounds fine to me, with the restriction that I would assume a min. cardinality of 2 to be applicable for this crossproduct, so at least 2 instruments make it a platform... at least one is not enough
AR:has_part is transitive, and transitive properties can't have cardinality constraints in OWL-DL. We can always put this particular constraint in the owl-full file.
We need to make this a defined class when the class software is in the ontologysuggested for deprecation https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178obsolete_platformtrueliquid chromatography mass spectrometry platformA liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI.OBI instrument branchOBI Instrument branchliquid chromatography mass spectrometry platformmicroarray platformA microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI.OBI Instrument branchOBI Instrument branchmicroarray platformratio of collected to emitted light10%A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative roleperson:Chris Stoeckertperson:Kevin ClancySubmitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txtratio of collected to emitted lightsoftware optimization objectiveSoftware_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software.Jennifer Fostelsoftware optimization objectivenotified body roleThe role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdfNotified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device DirectiveNotified Body (NB). A private institution charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive. This process, called Conformity Assessment, has EU-wide validity once completed by the NB.Person: Jennifer Fostelnotified bodyOBI, CDISCnotified body roleallotransplantationis the transplantation of organs between members of the same species.PlanAndPlannedProcess BranchOBI branch derivedallotransplantationgamma counterA Geiger counterA processed material which measures gamma radiationFrank Gibsonhttp://en.wikipedia.org/wiki/Gamma_countergamma countertrial monitor rolea responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a studyPerson:Jennifer Fosteltrial monitorCDISC definition: Person employed by the sponsor or CRO who is responsible for determining that a trial is being conducted in accordance with the protocol and GCP guidance. NOTE: A monitor's duties may include, but are not limited to, helping to plan and initiate a trial, assessing the conduct of trials, and assisting in data analysis, interpretation and extrapolation. Clinical Research Associate: Primary representative of the sponsor; monitors progress of investigator sites participating in a clinical study.trial monitor rolepositive reference substance roleMMS mutagena reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" responsePerson: Jennifer Fostelpositive reference substancepositive reference substance rolepolyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl etherPMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles.triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant propertiesPhilippe Rocca-Serraadapted from Wikipedia before possible import from CHEBIpolyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl etherinvestigationLung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigationa planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).Bjoern PetersOBI branch derivedCould add specific objective specificationFollowing OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core
editor = PRSstudyinvestigationevaluant roleWhen a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant roleRole call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")GROUP: Role BranchOBIFeb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.evaluant rolereporting party rolePerson who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htma study personnel role played by a party who reports the outcome of a study componentMO:submitter mapped to this term. So, alternative term 'submitter' was added.Jennifer Fostelreporting partysubmitterOBIreporting party roleassayAssay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branchmeasuringscientific observationOBI branch derivedstudy assayany methodassayquantitative confidence valueA data item which is used to indicate the degree of uncertainty about a measurement.person:Chris Stoeckertgroup:OBIquantitative confidence valuesample preparation for assayA sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.PlanAndPlannedProcess BranchstudyOBI branch derivedsample preparation for assaydiagnosis textual entitydiagnosis is an assessment of a disease or injury, its likely prognosis and treatment.Jennifer Fosteldiagnosis textual entityunplanned occurrence effecting an investigationEarthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants useda process which is external in origin to the investigation that has an impact on the outcome.PERSON: Bjoern PetersOBIunplanned occurrence effecting an investigationeMedical recordAn eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11.person:Jennifer Fostelarticle-without-pmid-or-doi:CDISCglossaryeMedical recordculture mediumA growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178
Modification made by JZ.Person: Jennifer Fostel, Jie ZhengOBIculture mediumelectronic case report tabulationAn electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators.person:Jennifer FostelCDISC glossaryelectronic case report tabulationpolystyrene tubePolystyrene tubes can be used to contain tissue culture cells during centrifgationa polystyrene tube is a test tube made of polystyrenePERSON: Chris StoeckertPERSON: Chris Stoeckertpolystyrene tubereagent roleBuffer, dye, a catalyst, a solvating agent.A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.PERSON:Matthew BrushreagentPERSON:Matthew BrushFeb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
(copied from ReO)
Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique.
Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated.
In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).reagent rolerole of regulator of chemical manufacturerEPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htma regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacturePerson: Jennifer Fostelregulator of chemical manufactureOBIrole of regulator of chemical manufacturerdetector reagent rolea role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus.19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instancesOne that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009detector reagent rolerole of certified IRB professionalCIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professionala role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USAPerson:Helen ParkinsonPerson:Jennifer Fostelcertified IRB professionalWEB: http://en.wikipedia.org/wiki/Certified_IRB_Professionalrole of certified IRB professionalpatient rolea hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778a role which inheres in a person and is realized by the process of being under the care of a physician or health care providerGROUP:Role BranchpatientOBI, CDISCCDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeablypatient rolematerial processingA cell lysis, production of a cloning vector, creating a buffer.A planned process which results in physical changes in a specified input materialPERSON: Bjoern PetersPERSON: Frank GibsonPERSON: Jennifer FostelPERSON: Melanie CourtotPERSON: Philippe Rocca Serramaterial transformationOBI branch derivedmaterial processingprotocol testing objectiveProtocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.Jennifer Fostelprotocol testing objectivestudy subject roleHuman subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study.
Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study.
Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.GROUP: Role BranchOBIFollowing OBI call November 2012,26th:
1. it was decided there was no need for moving the children class and making them siblings of study subject role.
2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study
This note closes the issue and validates the class definition to be part of the OBI core
editor = PRS
participant under investigation roleFirst subject treatedRat 1A; first enrolled patient to receive treatmentFirst subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the studyfirst subject treated. First subject who receives the test article or placebo in a clinical trial.Role BranchOBIobsolete_role of being first subject treatedtruemeasured expression levelExamples are quantified data from an expression microarray experiment, PCR measurements, etc.A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts.person:Chris StoeckertOBI Data Transformation branchmeasured expression levelresponsible party rolehe THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htma study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the studyPerson: Jennifer Fostelresponsible partyOBIresponsible party roleprincipal investigator rolea responsible party role played by a person responsible for the overall conduct of a studyPerson: Jennifer Fostelprincipal investigatorCDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC)principal investigator roletransplantationa protocol application to replace an organ or tissue of an organismPlanAndPlannedProcess BranchOBI branch derivedtransplantationbiological vector role1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission.Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector)falseGROUP: Role BranchOBI and Wikipedia6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoningbiological vector roletruepH indicator dye rolebromophenol blue has a pH indicator dye rolephenol red in RPMI; pH=4 indicator dye (also carries reference role)the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entityPerson: Jennifer FostelPerson:Helen ParkinsonpH indicator dyepH indicator dye rolespecimen roleliver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.blood taken from animal: animal continues in study, whereas blood has role specimen.
something taken from study subject, leaves the study and becomes the specimen.parasite example
- when parasite in people we study people, people are subjects and parasites are specimen
- when parasite extracted, they become subject in the following study
specimen can later be subject.GROUP: Role BranchOBIspecimen rolesequence feature identification objectiveSequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.Jennifer Fostelsequence feature identification objectiveintervention designPMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.Philppe Rocca-SerraOBI branch derivedintervention designworker rolePublic sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.htmla personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline"executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the studyPerson:Jennifer FostelworkerOBIworker roleBernoulli trialis an assay where the output data is a datum with one of two values denoted success and failure.PlanAndPlannedProcess BranchOBI branch derivedBernoulli trialgene listGene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.person:Chris Stoeckertgroup:OBIkind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object.gene listnumber of particles in subset500, 200, 0A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative roleperson:Kevin ClancySubmitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txtnumber of particles in subsetnumber of lost events electronic74, 0, 14 events lost due to data acquisition electronic coincidence.A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role.person:Kevin ClancySubmitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txtnumber of lost events electroniccalibration substance rolepH buffer used to calibrate a pH meter bears a calibration substance roleA reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performanceJennifer Fostelcalibration substance rolemolecular feature identification objectiveMolecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.Jennifer Fostelmolecular feature identification objectivehardware testing objectiveHardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner.Jennifer Fostelhardware testing objectiveincubatorIncubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cellsa device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlledFrank Gibsonhttp://www.medterms.com/script/main/art.asp?articlekey=18426incubatorlabel roleLabel role is a role which inheres in a material entity and which is realized in a detection of label assayMHB (9-26-12): consider deprecation of this class and replacement with REO:'molecular label role'Nucleotides synthesized with the incorporation of biotin were used to synthesize cDNA, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. the fluorochrome bears label role, the antibody bears detector role, the biotin bears reporter role. may need to change the terms following discussionneed to add a restriction that the material entity has the disposition / quality that permits it to be detected, and one way to say this (BP) is that the entity is such that an assay exists that detects the presence of the material entitywe need to sort out probe, detector and reporter. See https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1866458&amp;group_id=177891&amp;atid=886178Role BranchlabelOBIhttp://purl.obolibrary.org/obo/REO_0000171obsolete_label roletruebaseline participant roleSubject at time = 0; subject before a stress test.a reference participant role which is realized by making the reference to qualities at the start of the study or interventionPerson: Jennifer Fostelbaseline participantbaseline participant rolerole of independent data monitoring committeea trial monitor role charged recommending whether to continue, modify, or end the trialPerson: Jennifer Fostelindependent data monitoring committeerole of independent data monitoring committeepathologist rolea worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timelinePerson:Jennifer FostelPathologistpathologist rolesupernatant collection system harvesting framea device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125.Daniel Schobergooglesupernatant collection system harvesting framefilter papera device manufacture with the intent to provide a porous unsized paper used for filtering.Frank Gibsonsep:00107filter paper2cell co-culturingCulturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assayA material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.PlanAndPlannedProcess BranchOBI branch derivedcell co-culturingrole of Institutional Review BoardAn institutional review board/independent ethics committee (IRB/IEC) (also known as ethical review board) is a group that has been formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the alleged aim to protect the rights and welfare of the subjects. Wikipedia March 2008Animal protocol review boardthe role of a organization that is realized by members reviewing study designs for their agreement with regulationsPerson:Helen ParkinsonPerson:Jennifer FostelInternal Review BoardOBI, CDISCCDISC definition: institutional review board; independent ethics committee (IEC). An independent body (a review board or a committee, institutional, regional, national, or supranational) constituted of medical/scientific professionals and non-scientific members, whose responsibility it is to ensure the protection of the rights, safety and well-being of human subjects involved in a trial.role of Institutional Review BoardeSource documentan eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signaturesperson:Jennifer Fostelarticle-without-pmid-or-doi:CDISCglossaryeSource documentcrossover population rolea role realized when a participant serves as reference to itselfPerson: Jennifer Fostelcrossover populationcrossover population rolecomplete nutrient roleRat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htmA nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment.Person: Jennifer Fostelcomplete nutrientcomplete nutrient roleradiolabel rolea molecular label role which inheres in a material entity which is realized by the process of radioactivity detectionJennifer Fostelradiolabelradiolabel rolecDNA libraryPMID:6110205. collection of cDNA derived from mouse splenocytes.Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.PERSON: Luisa MontecchiPERSON: Philippe Rocca-SerraGROUP: PSIPRS: 22022008. class moved under population,
modification of definition and replacement of biomaterials in previous definition with 'material'
addition of has_role restrictioncDNA libraryelectronic case report formAn electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11.person:Jennifer FostelCDISC glossaryelectronic case report formplacebo rolePill consisting of inert materialsa negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substancePerson:Jennifer FostelplaceboCDISC definition placebo. A pharmaceutical preparation that does not contain the investigational agent. In blinded studies, it is generally prepared to be physically indistinguishable from the preparation containing the investigational product.placebo roleautotransplantationis the transplantation of tissue from one part of \nthe body to another in the same individual. )PlanAndPlannedProcess BranchOBI branch derivedautotransplantationparameter threshold0.01, 0.03A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative roleperson:Kevin ClancySubmitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txtparameter thresholdstudy group roleThe group of randomized participants that are assigned to a treatment arm of the triala study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocolJennifer Fostelstudy group populationstudy group rolep-valuePMID:19696660
in contrast to the in-vivo data AT-III increased significantly from
113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2).A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.May be outside the scope of OBI long term, is needed so is retainedPERSON:Chris StoeckertWEB: http://en.wikipedia.org/wiki/P-valuep-valuepopulationPMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms:
http://code.google.com/p/popcomm-ontology/PERSON: Philippe Rocca-Serraadapted from Oxford English Dictionnaryrem1: collection somehow always involve a selection processpopulationnuclear magnetic resonance 3D structure determination assayDetermining the binding of epitope-specific nanobody cAb-HuL5 to wild type human lysozyme by chemical shift perturbations in NMR spectra (Erwin De Genst, J Phys Chem B 2013).A 3D structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample.PlanAndPlannedProcess Branch, IEDBIEDBnuclear magnetic resonance 3D structure determination assayimaging assayAn imaging assay is an assay to produce a picture of an entity. definition_source: OBI.PlanAndPlannedProcess BranchOBI branch derivedimaging assayprotocol optimization objectiveProtocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol.Jennifer Fostelprotocol optimization objectiverole of pathology review boarda worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigationPerson: Jennifer Fostelpathology review boardrole of pathology review boardmicrotiter plateA microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)A microtiter_plate is a flat plate with multiple wells used as small test tubes.Melanie Courtotmicroplatehttp://en.wikipedia.org/wiki/Microtiter_platemicrotiter platerole of impartial witnessAccording to GCP , an impartial witness should be present for an
illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.htmla role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trialimpartial witness. A person, who is independent of the trial, who cannot be unfairly influenced by people involved with the trial, who attends the informed consent process if the subject or the subject's legally acceptable representative cannot read, and whoPerson: Helen ParkinsonPerson: Jennifer Fostelimpartial witnessrole of impartial witnesschromatin immunoprecipitationYang et al, Int J Clin Exp Pathol. 2015; 8(3): 2746–275 PMID:26045780. Cells were lysed and sonicated to shear DNA to lengths between 200-1000 bp. The sample was then incubated with antibodies against Acety-H3 to immunoprecipitate protein-DNA complexes using protein A agarose beads. The isolated protein-DNA complexes were treated with proteinase K digestion to remove histones. QPCR was then performed using primers specific for TGF-β1, MMP-9 and PI3K promoters at 95°C for 5 min, followed by 40 cycles at 95 °C for 20 s, 58°C for 20 s, and 72°C for 20 s. Each QPCR reaction was repeated in triplicate. QPCR was followed by a melt curve analysis to determine the reaction specificity. The relative gene expression was calculated using 2-ΔΔCt method.An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics.Bjoern Peters, Randi Vita, James A. OvertonChIPOBIchromatin immunoprecipitationbiological replicate roleA member of a dose-time group; a patient in a given arm of a triala reference participant role realized by equivalent treatment of participantsPerson:Jennifer Fostelbiological replicateOBIbiological replicate roleradioactivity detectionPlacing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material.An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material.PlanAndPlannedProcess Branch, IEDBIEDBradioactivity detectioninvestigation agent roleThe person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)GROUP: Role BranchinvestigatorOBIFeb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.study person rolePhilly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)investigation agent rolenutrient roleLuria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia.a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment.GROUP: Role branchnutrientWikipedia, feb 29, 200819 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment.nutrient roleDropoutEscaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study)Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role.Will be modelled as defined material, ouput of some 'dropout or withdrawal
process' instead of roleRole BranchOBIobsolete_dropout roletruehealth care provider rolea worker role of providing medical care either within or outside the study timelinePerson:Jennifer Fostelhealth care providerhealth care provider rolemethodology testing objectiveMethodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies.Jennifer Fostelmethodology testing objectiveanalytical cytology data fileFCS file, ACS file, foo.fcs, foo.ascA digital entity intended to capture data in analytical cytology domain.person:Chris Stoeckertgroup:Flow Cytometry communityanalytical cytology data fileproxy respondent roleProxy respondent is a worker role of describing patient's symptoms or condition to medical personnelJennifer Fostelproxy respondentproxy respondent rolefluorescence compensation matrix((1.053096, -0.22476), (-0.24877, 1.053096))A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix.person:Chris Stoeckertgroup:Flow Cytometry communityfluorescence compensation matrixnegative reference substance roleSaline solutiona reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" responsePerson: Jennifer Fostelnegative reference substancenegative reference substance rolerole of legally acceptable representativeParent of minor patient; Definition of legally acceptable representative
An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUEa role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial.legally acceptable representative. An individual or juridical or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject's participation in the clinical trial. [ICH, E6 Glossary]Person: Jennifer FostelPerson:Helen Parkinsonlegally acceptable representativeOBI, CDISCrole of legally acceptable representativeinvestigation results reportAn investigation report is a report on the results of an investigation.person:Chris Stoeckertgroup:OBIinvestigation results reportcellular feature identification objectiveCellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.Jennifer Fostelcellular feature identification objectivereference subject roleSaline treated rat; one of three identically-treated subjectsa reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or referenceJennifer Fostelreference participantOBIreference subject rolevital dye roletyptan blue has a vital dyeA dye role that is realized when used to detect live cells in an experiment2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178Person: Helen ParkinsonPerson: Jennifer Fostelvital dyevital dye roleBlinded medication115 patients received ipilimumab and blinded medicationInert pill shaped like aspirin tabletIs a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substanceWill be modelled using a blinding process and specified output blinded medication insteadJennifer FostelPerson:Helen Parkinsonobsolete_blinded medication roletruesub-investigator rolea worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timelinePerson: Jennifer Fostelsub-investigatorCDISC definition: Sub-investigator. Any member of the clinical trial team designated and supervised by the investigator at a trial site to perform critical trial-related procedures and/or to make important trial-related decisions (e.g., associates, residents, research fellows) [ICH] See associates, residents, research fellowssub-investigator roledata encodingstorage of measurement results from an assay into a text file, such asa documenting process to encode an information entity into a digital documentPlanAndPlannedProcess BranchOBI branch derivedWe (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIEdata encodingenzymatic cleavagePolymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzymePlanAndPlannedProcess BranchOBI branch derivedenzymatic cleavagehardware optimization objectiveHardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware.Jennifer Fostelhardware optimization objective_defined_materialPlace holder class, Utility class to gather the defined classesfalseSusanna SansoneOBI Biomaterial derivedobsolete_defined_materialtruetrial statistician rolea worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated.Person:Jennifer Fosteltrial statisticianCDISC definition: trial statistician. A statistician who has a combination of education/training and experience sufficient to implement the principles in the ICH E9 guidance and who is responsible for the statistical aspects of the trial. [ICH E9]trial statistician rolestandard errorA quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.person:Chris Stoeckertgroup:OBIsee P-Valuestandard errorantigen roleAntigen is a role played by material which when introduced into an immune-competent organism causes an immune responseAn antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigensRole BranchOBI9Mar09 waiting for discussion with immunology termsantigen rolesoftware testing objectiveSoftware_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software.Jennifer Fostelsoftware testing objectivesponsor rolea responsible party role involved with any of the following activities: initiating, managing and funding a studyPerson: Jennifer FostelsponsorCDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigatorssponsor roleorganizationPMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:
1) there are organization_member_roles (president, treasurer, branch
editor), with individual persons as bearers
2) there are organization_roles (employer, owner, vendor, patent holder)
3) an organization has a charter / rules / bylaws, which specify what roles
there are, how they should be realized, and how to modify the
charter/rules/bylaws themselves.
It is debatable what the organization itself is (some kind of dependent
continuant or an aggregate of people). This also determines who/what the
bearer of organization_roles' are. My personal favorite is still to define
organization as a kind of 'legal entity', but thinking it through leads to
all kinds of questions that are clearly outside the scope of OBI.
Interestingly enough, it does not seem to matter much where we place
organization itself, as long as we can subclass it (University, Corporation,
Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,
W3C, University of Oklahoma), and have it play roles.
This leads to my proposal: We define organization through the statements 1 -
3 above, but without an 'is a' statement for now. We can leave it in its
current place in the is_a hierarchy (material entity) or move it up to
'continuant'. We leave further clarifications to BFO, and close this issue
for now.PERSON: Alan RuttenbergPERSON: Bjoern PetersPERSON: Philippe Rocca-SerraPERSON: Susanna SansoneGROUP: OBIorganizationfeed rolePurina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment.Person: Jennifer FostelfeedOBIfeed roletechnical replicate roleAliquots of a tissue subjected to parallel assaystechnical replicate role is realized when two portions from one evaluant are used in replicate runs of an assayPerson: Jennifer Fosteltechnical replicatetechnical replicate roledye roleA molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest. Jennifer FosteldyeA substance used to color materials www.answers.com/topic/dye 19feb09dye roleclusterCluster of the lymphocytes population.A data set which is a subset of data that are a similar to each other in some way.person:Allysonperson:Chris Stoeckertgroup:OBIclustercohort roleIn statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study.Jennifer FostelWEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students.WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site).WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation.cohort roleartificially induced nucleic acid hybridizationwww.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdfIs a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules.PlanAndPlannedProcess BranchOBI branch derivedartificially induced nucleic acid hybridizationDNA extractionA DNA extraction is a nucleic acid extraction where the desired output material is DNA.PlanAndPlannedProcess BranchOBI branch derivedDNA extractionplanThe plan of researcher X to perform an experiment according to a protocol.A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.AR, BP, JM, MC, PRSbranch derivedplansample populationPatterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers.03/21/2010: BP, obsoleting this term, as it is duplicated by 'material sample'. Use that instead term instead, which now also has 'sample population' as an alternative label.PERSON: Jennifer FostelPERSON: Philippe Rocca-Serrarecruited populationGROUP: OBI Biomaterial Branchobsolete_sample populationtrueorganism feature identification objectiveOrganism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.Jennifer Fostelorganism feature identification objectivenumber of lost events computer0, 125, 787 events lost due to computer busy.A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative roleperson:Kevin ClancySubmitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txtnumber of lost events computerprotocolPCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.PlanAndPlannedProcess BranchOBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)study protocolprotocolrole of regulator of consumables and medical devicesFDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.htmla regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devicesPerson: Jennifer Fosteldrug regulatoy authorityOBI, CDISCrole of regulator of consumables and medical devicesadding a material entity into a targetInjecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.BPbranch derivedadding a material entity into a targetanalyte roleGlucose in blood (measured in an assay to determine the concentration of glucose).A role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant roleinterestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input rolepH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.qualities such as weight, color are not assayed but measured, so they do not fall into this category.GROUP: Role BranchOBIFeb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.analyte roledisease stageStage II breast cancer, The timepoint of recovery from a diseasea part of an occurrence of a disease process which is associated with position in the normal progression of the diseasePERSON: Bjoern petersdisease stage